1
|
Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
Collapse
Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Carrard J, Ratajczak F, Elsens J, Leroy C, Kong R, Geoffroy L, Comte A, Fournet G, Joseph B, Li X, Moebs-Sanchez S, Lejeune F. Identifying Potent Nonsense-Mediated mRNA Decay Inhibitors with a Novel Screening System. Biomedicines 2023; 11:2801. [PMID: 37893174 PMCID: PMC10604367 DOI: 10.3390/biomedicines11102801] [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: 09/18/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that degrades mRNAs carrying a premature termination codon. Its inhibition, alone or in combination with other approaches, could be exploited to develop therapies for genetic diseases caused by a nonsense mutation. This, however, requires molecules capable of inhibiting NMD effectively without inducing toxicity. We have built a new screening system and used it to identify and validate two new molecules that can inhibit NMD at least as effectively as cycloheximide, a reference NMD inhibitor molecule. These new NMD inhibitors show no cellular toxicity at tested concentrations and have a working concentration between 6.2 and 12.5 µM. We have further validated this NMD-inhibiting property in a physiopathological model of lung cancer in which the TP53 gene carries a nonsense mutation. These new molecules may potentially be of interest in the development of therapies for genetic diseases caused by a nonsense mutation.
Collapse
Affiliation(s)
- Julie Carrard
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fiona Ratajczak
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Joséphine Elsens
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Catherine Leroy
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Rebekah Kong
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Lucie Geoffroy
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Arnaud Comte
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, ICBMS, UMR 5246, Bâtiment Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Guy Fournet
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, ICBMS, UMR 5246, Bâtiment Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Benoît Joseph
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, ICBMS, UMR 5246, Bâtiment Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Xiubin Li
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, ICBMS, UMR 5246, Bâtiment Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Sylvie Moebs-Sanchez
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INSA Lyon, ICBMS, UMR 5246, Bâtiment Lederer, 1 Rue Victor Grignard, F-69622 Villeurbanne, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| |
Collapse
|
4
|
Benslimane N, Miressi F, Loret C, Richard L, Nizou A, Pyromali I, Faye PA, Favreau F, Lejeune F, Lia AS. Amlexanox: Readthrough Induction and Nonsense-Mediated mRNA Decay Inhibition in a Charcot-Marie-Tooth Model of hiPSCs-Derived Neuronal Cells Harboring a Nonsense Mutation in GDAP1 Gene. Pharmaceuticals (Basel) 2023; 16:1034. [PMID: 37513945 PMCID: PMC10385573 DOI: 10.3390/ph16071034] [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: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Nonsense mutations are involved in multiple peripheral neuropathies. These mutations induce the presence of a premature termination codon (PTC) at the mRNA level. As a result, a dysfunctional or truncated protein is synthesized, or even absent linked to nonsense-mediated mRNA degradation (NMD) system activation. Readthrough molecules or NMD inhibitors could be innovative therapies in these hereditary neuropathies, particularly molecules harboring the dual activity as amlexanox. Charcot-Marie-Tooth (CMT) is the most common inherited pathology of the peripheral nervous system, affecting 1 in 2500 people worldwide. Nonsense mutations in the GDAP1 gene have been associated with a severe form of CMT, prompting us to investigate the effect of readthrough and NMD inhibitor molecules. Although not clearly defined, GDAP1 could be involved in mitochondrial functions, such as mitophagy. We focused on the homozygous c.581C>G (p.Ser194*) mutation inducing CMT2H using patient human induced pluripotent stem cell (hiPSC)-derived neuronal cells. Treatment during 20 h with 100 µM of amlexanox on this cell model stabilized GDAP1 mRNAs carrying UGA-PTC and induced a restoration of the mitochondrial morphology. These results highlight the potential of readthrough molecules associated to NMD inhibitors for the treatment of genetic alterations in CMT, opening the way for future investigations and a potential therapy.
Collapse
Affiliation(s)
- Nesrine Benslimane
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
| | - Federica Miressi
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
| | - Camille Loret
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
| | - Laurence Richard
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
- CHU Limoges, Service de Neurologie, F-87000 Limoges, France
| | - Angélique Nizou
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
| | - Ioanna Pyromali
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
| | - Pierre-Antoine Faye
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
- Centre Hospitalier Universitaire (CHU) Limoges, Service de Biochimie et de Génétique Moléculaire, F-87000 Limoges, France
| | - Frédéric Favreau
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
- Centre Hospitalier Universitaire (CHU) Limoges, Service de Biochimie et de Génétique Moléculaire, F-87000 Limoges, France
| | - Fabrice Lejeune
- CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France
| | - Anne-Sophie Lia
- NeurIT UR 20218, GEIST Institute, Faculté de Médecine de Limoges, University of Limoges, F-87000 Limoges, France
- Centre Hospitalier Universitaire (CHU) Limoges, Service de Biochimie et de Génétique Moléculaire, F-87000 Limoges, France
- Centre Hospitalo-Universitaire (CHU) Limoges, UF de Bioinformatique, F-87000 Limoges, France
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Gil-Martínez J, Bernardo-Seisdedos G, Mato JM, Millet O. The use of pharmacological chaperones in rare diseases caused by reduced protein stability. Proteomics 2022; 22:e2200222. [PMID: 36205620 DOI: 10.1002/pmic.202200222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Rare diseases are most often caused by inherited genetic disorders that, after translation, will result in a protein with altered function. Decreased protein stability is the most frequent mechanism associated with a congenital pathogenic missense mutation and it implies the destabilization of the folded conformation in favour of unfolded or misfolded states. In the cellular context and when experimental data is available, a mutant protein with altered thermodynamic stability often also results in impaired homeostasis, with the deleterious accumulation of protein aggregates, metabolites and/or metabolic by-products. In the last decades, a significant effort has enabled the characterization of rare diseases associated to protein stability defects and triggered the development of innovative therapeutic intervention lines, say, the use of pharmacological chaperones to correct the intracellular impaired homeostasis. Here, we review the current knowledge on rare diseases caused by reduced protein stability, paying special attention to the thermodynamic aspects of the protein destabilization, also focusing on some examples where pharmacological chaperones are being tested.
Collapse
Affiliation(s)
- Jon Gil-Martínez
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
| | | | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,ATLAS Molecular Pharma, Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
8
|
2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases. Proc Natl Acad Sci U S A 2022; 119:e2122004119. [PMID: 35994666 PMCID: PMC9436315 DOI: 10.1073/pnas.2122004119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Nonsense mutations account for approximately 11% of all described gene lesions causing human inherited diseases. This premature termination codon (PTC) leads to the premature arrest of translation that generates a truncated peptide and the degradation of the corresponding mRNA through the nonsense-mediated mRNA decay (NMD) pathway. The possibility of restoring the protein expression by promoting PTC readthrough using drugs appears to be an important therapeutic strategy. Unfortunately, this strategy is limited by the small number of molecules known to promote PTC readthrough without affecting normal translation termination. In this work, we identify a new molecule, TLN468, that promotes a high level of PTC readthrough without a detectable effect on normal stop codons. Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).
Collapse
|
9
|
Rastogi R, Stenson PD, Cooper DN, Bejerano G. X-CAP improves pathogenicity prediction of stopgain variants. Genome Med 2022; 14:81. [PMID: 35906703 PMCID: PMC9338606 DOI: 10.1186/s13073-022-01078-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Stopgain substitutions are the third-largest class of monogenic human disease mutations and often examined first in patient exomes. Existing computational stopgain pathogenicity predictors, however, exhibit poor performance at the high sensitivity required for clinical use. Here, we introduce a new classifier, termed X-CAP, which uses a novel training methodology and unique feature set to improve the AUROC by 18% and decrease the false-positive rate 4-fold on large variant databases. In patient exomes, X-CAP prioritizes causal stopgains better than existing methods do, further illustrating its clinical utility. X-CAP is available at https://github.com/bejerano-lab/X-CAP .
Collapse
Affiliation(s)
- Ruchir Rastogi
- grid.168010.e0000000419368956Department of Computer Science, Stanford University, Stanford, USA
| | - Peter D. Stenson
- grid.5600.30000 0001 0807 5670Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N. Cooper
- grid.5600.30000 0001 0807 5670Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, USA. .,Department of Developmental Biology, Stanford University, Stanford, USA. .,Department of Pediatrics, Stanford University, Stanford, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, USA.
| |
Collapse
|
10
|
Yaméogo P, Duchêne BL, Majeau N, Tremblay JP. CRISPR-SCReT (CRISPR-Stop Codon Read Through) method to control Cas9 expression for gene editing. Gene Ther 2021; 29:171-177. [PMID: 34593991 DOI: 10.1038/s41434-021-00297-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022]
Abstract
CRISPR/Cas9 has paved the way for the development of therapies that correct genetic mutations. However, constitutive expression of the Cas9 gene can increase off-target mutations and induce an immune response against the Cas9 protein. To limit the time during which the Cas9 nuclease is expressed, we proposed a simple drug inducible system. The approach consists of introducing a premature termination codon (PTC) in the Cas9 gene and subsequently treating with an aminoglycoside drug, which allows readthrough of the complete protein. To validate that system, HEK293T cells were co-transfected with a PX458 plasmid, which was mutated to introduce a PTC in the SpCas9 gene and two sgRNAs targeting the DMD gene (exons 50 and 54). Cells were treated with different doses of geneticin (G418) for 48 h. Western blot confirmed that the Cas9 protein expression, which was shut down by the PTC mutation, can be induced by the drug. The hybrid exon 50-54 formed by the deletion of part of the DMD gene was detected by PCR only in the cells treated with G418. The approach was also used successfully with CjCas9 to edit the FXN gene. Our results show that it is possible to control SpCas9 and CjCas9 expression by CRISPR-SCReT (CRISPR-Stop Codon Read Through) method.
Collapse
Affiliation(s)
- Pouiré Yaméogo
- Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada.,Département de Médecine Moléculaire, Université Laval, Québec City, QC, Canada
| | - Benjamin L Duchêne
- Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada.,Département de Médecine Moléculaire, Université Laval, Québec City, QC, Canada
| | - Nathalie Majeau
- Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada.,Département de Médecine Moléculaire, Université Laval, Québec City, QC, Canada
| | - Jacques P Tremblay
- Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada. .,Département de Médecine Moléculaire, Université Laval, Québec City, QC, Canada.
| |
Collapse
|
11
|
Abstract
Since the cloning of the CFTR gene 30 years ago, research aiming at understanding how CFTR mutations translate to abnormal synthesis or function of the CFTR protein has opened the way to genomically-guided therapy to improve CFTR function. A CFTR potentiator to enhance CFTR channel function has been approved in 2012 for specific and quite rare mutations. Subsequently, combinations of a corrector to increase CFTR expression at the cell membrane, plus a potentiator, have been approved for patients homozygous for the p.Phe508del mutation. To obtain robust correction of CFTR, new combinations of drugs are being studied. A triple combination associating two correctors and one potentiator is very promising and if data of clinical trials are confirmed, it could be a robust and well tolerated CFTR modulator for patients bearing at least one p.Phe508del mutation. Many other strategies are also in development to make these genomically-guided treatments available to all patients with CF. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
Collapse
Affiliation(s)
- I Fajac
- AP-HP, Hôpital Cochin, Service de Physiologie et Explorations Fonctionnelles, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - E Girodon
- APHP, Centre-Université de Paris, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| |
Collapse
|
12
|
Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| |
Collapse
|
13
|
Morais P, Adachi H, Yu YT. Suppression of Nonsense Mutations by New Emerging Technologies. Int J Mol Sci 2020; 21:ijms21124394. [PMID: 32575694 PMCID: PMC7352488 DOI: 10.3390/ijms21124394] [Citation(s) in RCA: 28] [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: 05/28/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
Nonsense mutations often result from single nucleotide substitutions that change a sense codon (coding for an amino acid) to a nonsense or premature termination codon (PTC) within the coding region of a gene. The impact of nonsense mutations is two-fold: (1) the PTC-containing mRNA is degraded by a surveillance pathway called nonsense-mediated mRNA decay (NMD) and (2) protein translation stops prematurely at the PTC codon, and thus no functional full-length protein is produced. As such, nonsense mutations result in a large number of human diseases. Nonsense suppression is a strategy that aims to correct the defects of hundreds of genetic disorders and reverse disease phenotypes and conditions. While most clinical trials have been performed with small molecules, there is an increasing need for sequence-specific repair approaches that are safer and adaptable to personalized medicine. Here, we discuss recent advances in both conventional strategies as well as new technologies. Several of these will soon be tested in clinical trials as nonsense therapies, even if they still have some limitations and challenges to overcome.
Collapse
Affiliation(s)
- Pedro Morais
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, The Netherlands;
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
- Correspondence: ; Tel.: +1-(585)-275-1271; Fax: +1-(585)-275-6007
| |
Collapse
|
14
|
2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations. Nat Commun 2020; 11:1509. [PMID: 32198346 PMCID: PMC7083880 DOI: 10.1038/s41467-020-15140-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2′-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations. Nonsense mutations can be corrected by several molecules that activate readthrough of premature termination codon. Here, the authors report that 2,6-diaminopurine efficiently corrects UGA nonsense mutations with no significant toxicity.
Collapse
|
15
|
Didiasova M, Banning A, Brennenstuhl H, Jung-Klawitter S, Cinquemani C, Opladen T, Tikkanen R. Succinic Semialdehyde Dehydrogenase Deficiency: An Update. Cells 2020; 9:cells9020477. [PMID: 32093054 PMCID: PMC7072817 DOI: 10.3390/cells9020477] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is a genetic disorder that results from the aberrant metabolism of the neurotransmitter γ-amino butyric acid (GABA). The disease is caused by impaired activity of the mitochondrial enzyme succinic semialdehyde dehydrogenase. SSADH-D manifests as varying degrees of mental retardation, autism, ataxia, and epileptic seizures, but the clinical picture is highly heterogeneous. So far, there is no approved curative therapy for this disease. In this review, we briefly summarize the molecular genetics of SSADH-D, the past and ongoing clinical trials, and the emerging features of the molecular pathogenesis, including redox imbalance and mitochondrial dysfunction. The main aim of this review is to discuss the potential of further therapy approaches that have so far not been tested in SSADH-D, such as pharmacological chaperones, read-through drugs, and gene therapy. Special attention will also be paid to elucidating the role of patient advocacy organizations in facilitating research and in the communication between researchers and patients.
Collapse
Affiliation(s)
- Miroslava Didiasova
- Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany; (M.D.); (A.B.)
| | - Antje Banning
- Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany; (M.D.); (A.B.)
| | - Heiko Brennenstuhl
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, University Children’s Hospital Heidelberg, 69120 Heidelberg, Germany; (H.B.); (S.J.-K.); (T.O.)
| | - Sabine Jung-Klawitter
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, University Children’s Hospital Heidelberg, 69120 Heidelberg, Germany; (H.B.); (S.J.-K.); (T.O.)
| | | | - Thomas Opladen
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, University Children’s Hospital Heidelberg, 69120 Heidelberg, Germany; (H.B.); (S.J.-K.); (T.O.)
| | - Ritva Tikkanen
- Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany; (M.D.); (A.B.)
- Correspondence: ; Tel.: +49-641-9947-420
| |
Collapse
|
16
|
Martorell L, Cortina V, Parra R, Barquinero J, Vidal F. Variable readthrough responsiveness of nonsense mutations in hemophilia A. Haematologica 2020; 105:508-518. [PMID: 31197069 PMCID: PMC7012483 DOI: 10.3324/haematol.2018.212118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/11/2019] [Indexed: 12/26/2022] Open
Abstract
Readthrough therapy relies on the use of small molecules that enable premature termination codons in mRNA open reading frames to be misinterpreted by the translation machinery, thus allowing the generation of full-length, potentially functional proteins from mRNA carrying nonsense mutations. In patients with hemophilia A, nonsense mutations potentially sensitive to readthrough agents represent approximately 16% of the point mutations. The aim of this study was to measure the readthrough effect of different compounds and to analyze the influence of premature termination codon context in selected nonsense mutations causing hemophilia A. To this end, primary fibroblasts from three patients with hemophilia A caused by nonsense mutations (p.W1586X, p.Q1636X and p.R1960X) and Chinese hamster ovary (CHO) cells transfected with 12 different plasmids encoding mutated F8 (p.Q462X, p.Q1705X, p.Q1764X, p.W274X, p.W1726X, p.W2015X, p.W2131X, p.R1715X, p.R1822X, p.R1960X, p.R2071X and p.R2228X) were treated with gentamicin, geneticin, PTC124, RTC13 or RTC14. Responses were assessed by analyzing not only F8 mRNA expression and FVIII biosynthesis (FVIII antigen by ELISA, western blot and immunofluorescence) but also the FVIII activity (by chromogenic assay). In the patients' fibroblasts, readthrough agents neither stabilized F8 mRNA nor increased FVIII protein or activity to detectable levels. In CHO cells, only in five of the 12 F8 variants, readthrough treatment increased both FVIII antigen and activity levels, which was associated with a reduction in intracellular accumulation of truncated forms and an increase in full-length proteins. These results provide experimental evidence of genetic context dependence of nonsense suppression by readthrough agents and of factors predicting responsiveness.
Collapse
Affiliation(s)
- Lluis Martorell
- Gene and Cell Therapy Laboratory, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona (UAB).,Congenital Coagulopathies Laboratory, Banc de Sang i Teixits (BST)
| | - Vicente Cortina
- Vall d'Hebron Core Laboratory (Section of Thrombosis and Haemostasis), Hospital Vall d'Hebron
| | | | - Jordi Barquinero
- Gene and Cell Therapy Laboratory, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona (UAB)
| | - Francisco Vidal
- Congenital Coagulopathies Laboratory, Banc de Sang i Teixits (BST) .,Molecular Diagnosis and Therapy Unit, VHIR-UAB.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Barcelona, Spain
| |
Collapse
|
17
|
Cabrini G. Innovative Therapies for Cystic Fibrosis: The Road from Treatment to Cure. Mol Diagn Ther 2019; 23:263-279. [PMID: 30478715 DOI: 10.1007/s40291-018-0372-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF), a life-threatening multiorgan genetic disease, is facing a new era of research and development using innovative gene-directed personalized therapies. The priority organ to cure is the lung, which suffers recurrent and chronic bacterial infection and inflammation since infancy, representing the main cause of morbidity and precocious mortality of these individuals. After the disappointing failure of gene-replacement approaches using gene therapy vectors, no single drug is presently available to repair all the CF gene defects. The impressive number of different CF gene mutations is now tackled with different chemical and biotechnological tools tailored to the specific molecular derangements, thanks to the extensive knowledge acquired over many years on the mechanisms of CF cell and organ pathology. This review provides an overview and recalls both the successes and limitations of the different experimental approaches, such as high-throughput screening on chemical libraries to discover CF gene correctors and potentiators, dual-acting compounds, read-through molecules, splicing defect repairing tools, cystic fibrosis transmembrane conductance regulator (CFTR) "amplifiers," CFTR interactome modulators and the first gene editing attempts.
Collapse
Affiliation(s)
- Giulio Cabrini
- Laboratory of Molecular Pathology, University Hospital, Verona, Italy. .,Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
| |
Collapse
|
18
|
McHugh DR, Steele MS, Valerio DM, Miron A, Mann RJ, LePage DF, Conlon RA, Cotton CU, Drumm ML, Hodges CA. A G542X cystic fibrosis mouse model for examining nonsense mutation directed therapies. PLoS One 2018; 13:e0199573. [PMID: 29924856 PMCID: PMC6010256 DOI: 10.1371/journal.pone.0199573] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/08/2018] [Indexed: 12/22/2022] Open
Abstract
Nonsense mutations are present in 10% of patients with CF, produce a premature termination codon in CFTR mRNA causing early termination of translation, and lead to lack of CFTR function. There are no currently available animal models which contain a nonsense mutation in the endogenous Cftr locus that can be utilized to test nonsense mutation therapies. In this study, we create a CF mouse model carrying the G542X nonsense mutation in Cftr using CRISPR/Cas9 gene editing. The G542X mouse model has reduced Cftr mRNA levels, demonstrates absence of CFTR function, and displays characteristic manifestations of CF mice such as reduced growth and intestinal obstruction. Importantly, CFTR restoration is observed in G542X intestinal organoids treated with G418, an aminoglycoside with translational readthrough capabilities. The G542X mouse model provides an invaluable resource for the identification of potential therapies of CF nonsense mutations as well as the assessment of in vivo effectiveness of these potential therapies targeting nonsense mutations.
Collapse
Affiliation(s)
- Daniel R. McHugh
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Miarasa S. Steele
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dana M. Valerio
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Rachel J. Mann
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - David F. LePage
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ronald A. Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Calvin U. Cotton
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mitchell L. Drumm
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Craig A. Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| |
Collapse
|