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Cook AL, Sur S, Dobbyn L, Watson E, Cohen JD, Ptak B, Lee BS, Paul S, Hsiue E, Popoli M, Vogelstein B, Papadopoulos N, Bettegowda C, Gabrielson K, Zhou S, Kinzler KW, Wyhs N. Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.28.573594. [PMID: 38234817 PMCID: PMC10793421 DOI: 10.1101/2023.12.28.573594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1's phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro . Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence Summary Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.
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García-Blay Ó, Verhagen PGA, Martin B, Hansen MMK. Exploring the role of transcriptional and post-transcriptional processes in mRNA co-expression. Bioessays 2023; 45:e2300130. [PMID: 37926676 DOI: 10.1002/bies.202300130] [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: 07/12/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023]
Abstract
Co-expression of two or more genes at the single-cell level is usually associated with functional co-regulation. While mRNA co-expression-measured as the correlation in mRNA levels-can be influenced by both transcriptional and post-transcriptional events, transcriptional regulation is typically considered dominant. We review and connect the literature describing transcriptional and post-transcriptional regulation of co-expression. To enhance our understanding, we integrate four datasets spanning single-cell gene expression data, single-cell promoter activity data and individual transcript half-lives. Confirming expectations, we find that positive co-expression necessitates promoter coordination and similar mRNA half-lives. Surprisingly, negative co-expression is favored by differences in mRNA half-lives, contrary to initial predictions from stochastic simulations. Notably, this association manifests specifically within clusters of genes. We further observe a striking compensation between promoter coordination and mRNA half-lives, which additional stochastic simulations suggest might give rise to the observed co-expression patterns. These findings raise intriguing questions about the functional advantages conferred by this compensation between distal kinetic steps.
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Affiliation(s)
- Óscar García-Blay
- Institute for Molecules and Materials, Radboud University, AJ, Nijmegen, the Netherlands
| | - Pieter G A Verhagen
- Institute for Molecules and Materials, Radboud University, AJ, Nijmegen, the Netherlands
| | - Benjamin Martin
- Institute for Molecules and Materials, Radboud University, AJ, Nijmegen, the Netherlands
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, AJ, Nijmegen, the Netherlands
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3
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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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Leroy C, Spelier S, Essonghe NC, Poix V, Kong R, Gizzi P, Bourban C, Amand S, Bailly C, Guilbert R, Hannebique D, Persoons P, Arhant G, Prévotat A, Reix P, Hubert D, Gérardin M, Chamaillard M, Prevarskaya N, Rebuffat S, Shapovalov G, Beekman J, Lejeune F. Use of 2,6-diaminopurine as a potent suppressor of UGA premature stop codons in cystic fibrosis. Mol Ther 2023; 31:970-985. [PMID: 36641622 PMCID: PMC10124085 DOI: 10.1016/j.ymthe.2023.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/10/2022] [Accepted: 01/12/2023] [Indexed: 01/16/2023] Open
Abstract
Nonsense mutations are responsible for around 10% of cases of genetic diseases, including cystic fibrosis. 2,6-diaminopurine (DAP) has recently been shown to promote efficient readthrough of UGA premature stop codons. In this study, we show that DAP can correct a nonsense mutation in the Cftr gene in vivo in a new CF mouse model, in utero, and through breastfeeding, thanks, notably, to adequate pharmacokinetic properties. DAP turns out to be very stable in plasma and is distributed throughout the body. The ability of DAP to correct various endogenous UGA nonsense mutations in the CFTR gene and to restore its function in mice, in organoids derived from murine or patient cells, and in cells from patients with cystic fibrosis reveals the potential of such readthrough-stimulating molecules in developing a therapeutic approach. The fact that correction by DAP of certain nonsense mutations reaches a clinically relevant level, as judged from previous studies, makes the use of this compound all the more attractive.
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Affiliation(s)
- Catherine Leroy
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Sacha Spelier
- 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, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Nadège Charlene Essonghe
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Virginie Poix
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Rebekah Kong
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Patrick Gizzi
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR 3286 CNRS-Université de Strasbourg, 67404 Illkirch, France
| | - Claire Bourban
- Plateforme de Chimie Biologique Intégrative de Strasbourg, UAR 3286 CNRS-Université de Strasbourg, 67404 Illkirch, France
| | - Séverine Amand
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Christine Bailly
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - Romain Guilbert
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - David Hannebique
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - Philippe Persoons
- Institut Pasteur de Lille-PLEHTA (Plateforme d'Expérimentation et de Haute Technologie Animale), 59019 Lille, France
| | - Gwenaëlle Arhant
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France
| | - Anne Prévotat
- University Lille, Clinique des Maladies Respiratoires, CRCM Hôpital Calmette, CHRU Lille, 59000 Lille, France
| | - Philippe Reix
- CRCM Pédiatrique Lyon, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, UMR 5558 (EMET), CNRS, LBBE, Université de Lyon, 69622 Villeurbanne, France
| | - Dominique Hubert
- Pulmonary Department and Adult CF Centre, Cochin Hospital, AP-HP, Paris, France
| | - Michèle Gérardin
- CF Pediatric Centre, Robert Debré Hospital, AP-HP, 75019 Paris, France
| | - Mathias Chamaillard
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France
| | - Natalia Prevarskaya
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 Rue Cuvier, 75005 Paris, France
| | - George Shapovalov
- University Lille, INSERM, U1003-PHYCEL-Physiologie Cellulaire, 59000 Lille, France; Laboratory of Excellence, Ion Channels Science and Therapeutics, 59655 Villeneuve d'Ascq, France
| | - Jeffrey Beekman
- 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, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Fabrice Lejeune
- University Lille, CNRS, INSERM, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France; Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, 59000 Lille, France.
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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Abbouda A, Avogaro F, Moosajee M, Vingolo EM. Update on Gene Therapy Clinical Trials for Choroideremia and Potential Experimental Therapies. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:64. [PMID: 33445564 PMCID: PMC7826687 DOI: 10.3390/medicina57010064] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/26/2020] [Accepted: 01/07/2021] [Indexed: 12/27/2022]
Abstract
Background and objectives: Choroideremia (CHM) is an X-linked recessive chorioretinal dystrophy caused by mutations involving the CHM gene. Gene therapy has entered late-phase clinical trials, although there have been variable results. This review gives a summary on the outcomes of phase I/II CHM gene therapy trials and describes other potential experimental therapies. Materials and Methods: A Medline (National Library of Medicine, Bethesda, MD, USA) search was performed to identify all articles describing gene therapy treatments available for CHM. Results: Five phase I/II clinical trials that reported subretinal injection of adeno-associated virus Rab escort protein 1 (AAV2.REP1) vector in CHM patients were included. The Oxford study (NCT01461213) included 14 patients; a median gain of 5.5 ± 6.8 SD (-6 min, 18 max) early treatment diabetic retinopathy study (ETDRS) letters was reported. The Tubingen study (NCT02671539) included six patients; only one patient had an improvement of 17 ETDRS letters. The Alberta study (NCT02077361) enrolled six patients, and it reported a minimal vision change, except for one patient who gained 15 ETDRS letters. Six patients were enrolled in the Miami trial (NCT02553135), which reported a median gain of 2 ± 4 SD (-1 min, 10 max) ETDRS letters. The Philadelphia study (NCT02341807) included 10 patients; best corrected visual acuity (BCVA) returned to baseline in all by one-year follow-up, but one patient had -17 ETDRS letters from baseline. Overall, 40 patients were enrolled in trials, and 34 had 2 years of follow-up, with a median gain of 1.5 ± 7.2 SD (-14 min, 18 max) in ETDRS letters. Conclusions: The primary endpoint, BCVA following gene therapy in CHM, showed a marginal improvement with variability between trials. Optimizing surgical technique and pre-, peri-, and post-operative management with immunosuppressants to minimize any adverse ocular inflammatory events could lead to reduced incidence of complications. The ideal therapeutic window needs to be addressed to ensure that the necessary cell types are adequately transduced, minimizing viral toxicity, to prolong long-term transgenic potential. Long-term efficacy will be addressed by ongoing studies.
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Affiliation(s)
| | - Filippo Avogaro
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p.le A. Moro 5, 00185 Rome, Italy;
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK;
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Enzo Maria Vingolo
- Fiorini Hospital Terracina AUSL, 04019 Terracina, Latina, Italy;
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p.le A. Moro 5, 00185 Rome, Italy;
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Way CM, Lima Cunha D, Moosajee M. Translational readthrough inducing drugs for the treatment of inherited retinal dystrophies. EXPERT REVIEW OF OPHTHALMOLOGY 2020. [DOI: 10.1080/17469899.2020.1762489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christopher M Way
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Dulce Lima Cunha
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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8
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Sarkar H, Mitsios A, Smart M, Skinner J, Welch AA, Kalatzis V, Coffey PJ, Dubis AM, Webster AR, Moosajee M. Nonsense-mediated mRNA decay efficiency varies in choroideremia providing a target to boost small molecule therapeutics. Hum Mol Genet 2019; 28:1865-1871. [PMID: 30689859 PMCID: PMC6522067 DOI: 10.1093/hmg/ddz028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Choroideremia (CHM) is an x-linked recessive chorioretinal dystrophy, with 30% caused by nonsense mutations in the CHM gene resulting in an in-frame premature termination codon (PTC). Nonsense-mediated mRNA decay (NMD) is the cell's natural surveillance mechanism that detects and destroys PTC-containing transcripts, with UPF1 being the central NMD modulator. NMD efficiency can be variable amongst individuals with some transcripts escaping destruction, leading to the production of a truncated non-functional or partially functional protein. Nonsense suppression drugs, such as ataluren, target these transcripts and read-through the PTC, leading to the production of a full length functional protein. Patients with higher transcript levels are considered to respond better to these drugs, as more substrate is available for read-through. Using Quantitative reverse transcription PCR (RT-qPCR), we show that CHM mRNA expression in blood from nonsense mutation CHM patients is 2.8-fold lower than controls, and varies widely amongst patients, with 40% variation between those carrying the same UGA mutation [c.715 C>T; p.(R239*)]. These results indicate that although NMD machinery is at work, efficiency is highly variable and not wholly dependent on mutation position. No significant difference in CHM mRNA levels was seen between two patients' fibroblasts and their induced pluripotent stem cell-derived retinal pigment epithelium. There was no correlation between CHM mRNA expression and genotype, phenotype or UPF1 transcript levels. NMD inhibition with caffeine was shown to restore CHM mRNA transcripts to near wild-type levels. Baseline mRNA levels may provide a prognostic indicator for response to nonsense suppression therapy, and caffeine may be a useful adjunct to enhance treatment efficacy where indicated.
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Affiliation(s)
- Hajrah Sarkar
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Andreas Mitsios
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Matthew Smart
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Jane Skinner
- Department of Public Health & Primary Care, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Ailsa A Welch
- Department of Public Health & Primary Care, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, Montpellier Cedex, France
| | - Peter J Coffey
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Adam M Dubis
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Department of Ophthalmology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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Unfolded protein response is an early, non-critical event during hepatic stellate cell activation. Cell Death Dis 2019; 10:98. [PMID: 30718473 PMCID: PMC6362073 DOI: 10.1038/s41419-019-1327-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
Hepatic stellate cells activate upon liver injury and help at restoring damaged tissue by producing extracellular matrix proteins. A drastic increase in matrix proteins results in liver fibrosis and we hypothesize that this sudden increase leads to accumulation of proteins in the endoplasmic reticulum and its compensatory mechanism, the unfolded protein response. We indeed observe a very early, but transient induction of unfolded protein response genes during activation of primary mouse hepatic stellate cells in vitro and in vivo, prior to induction of classical stellate cell activation genes. This unfolded protein response does not seem sufficient to drive stellate cell activation on its own, as chemical induction of endoplasmic reticulum stress with tunicamycin in 3D cultured, quiescent stellate cells is not able to induce stellate cell activation. Inhibition of Jnk is important for the transduction of the unfolded protein response. Stellate cells isolated from Jnk knockout mice do not activate as much as their wild-type counterparts and do not have an induced expression of unfolded protein response genes. A timely termination of the unfolded protein response is essential to prevent endoplasmic reticulum stress-related apoptosis. A pathway known to be involved in this termination is the non-sense-mediated decay pathway. Non-sense-mediated decay inhibitors influence the unfolded protein response at early time points during stellate cell activation. Our data suggest that UPR in HSCs is differentially regulated between acute and chronic stages of the activation process. In conclusion, our data demonstrates that the unfolded protein response is a JNK1-dependent early event during hepatic stellate cell activation, which is counteracted by non-sense-mediated decay and is not sufficient to drive the stellate cell activation process. Therapeutic strategies based on UPR or NMD modulation might interfere with fibrosis, but will remain challenging because of the feedback mechanisms between the stress pathways.
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Mitsios A, Dubis AM, Moosajee M. Choroideremia: from genetic and clinical phenotyping to gene therapy and future treatments. Ther Adv Ophthalmol 2018; 10:2515841418817490. [PMID: 30627697 PMCID: PMC6311551 DOI: 10.1177/2515841418817490] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/05/2018] [Indexed: 11/15/2022] Open
Abstract
Choroideremia is an X-linked inherited chorioretinal dystrophy leading to blindness by late adulthood. Choroideremia is caused by mutations in the CHM gene which encodes Rab escort protein 1 (REP1), an ubiquitously expressed protein involved in intracellular trafficking and prenylation activity. The exact site of pathogenesis remains unclear but results in degeneration of the photoreceptors, retinal pigment epithelium and choroid. Animal and stem cell models have been used to study the molecular defects in choroideremia and test effectiveness of treatment interventions. Natural history studies of choroideremia have provided additional insight into the clinical phenotype of the condition and prepared the way for clinical trials aiming to investigate the safety and efficacy of suitable therapies. In this review, we provide a summary of the current knowledge on the genetics, pathophysiology, clinical features and therapeutic strategies that might become available for choroideremia in the future, including gene therapy, stem cell treatment and small-molecule drugs with nonsense suppression action.
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Affiliation(s)
- Andreas Mitsios
- Institute of Ophthalmology, University College London, London, UK
| | - Adam M Dubis
- Institute of Ophthalmology, University College London, London, UK
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, UK
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Dabrowski M, Bukowy-Bieryllo Z, Zietkiewicz E. Advances in therapeutic use of a drug-stimulated translational readthrough of premature termination codons. Mol Med 2018; 24:25. [PMID: 30134808 PMCID: PMC6016875 DOI: 10.1186/s10020-018-0024-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/31/2022] Open
Abstract
Premature termination codons (PTCs) in the coding regions of mRNA lead to the incorrect termination of translation and generation of non-functional, truncated proteins. Translational readthrough of PTCs induced by pharmaceutical compounds is a promising way of restoring functional protein expression and reducing disease symptoms, without affecting the genome or transcriptome of the patient. While in some cases proven effective, the clinical use of readthrough-inducing compounds is still associated with many risks and difficulties. This review focuses on problems directly associated with compounds used to stimulate PTC readthrough, such as their interactions with the cell and organism, their toxicity and bioavailability (cell permeability; tissue deposition etc.). Various strategies designed to overcome these problems are presented.
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Affiliation(s)
- Maciej Dabrowski
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland
| | | | - Ewa Zietkiewicz
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland.
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12
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Salvatori F, Pappadà M, Breveglieri G, D'Aversa E, Finotti A, Lampronti I, Gambari R, Borgatti M. UPF1 silenced cellular model systems for screening of read-through agents active on β 039 thalassemia point mutation. BMC Biotechnol 2018; 18:28. [PMID: 29764417 PMCID: PMC5952824 DOI: 10.1186/s12896-018-0435-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nonsense mutations promote premature translational termination, introducing stop codons within the coding region of mRNAs and causing inherited diseases, including thalassemia. For instance, in β039 thalassemia the CAG (glutamine) codon is mutated to the UAG stop codon, leading to premature translation termination and to mRNA destabilization through the well described NMD (nonsense-mediated mRNA decay). In order to develop an approach facilitating translation and, therefore, protection from NMD, ribosomal read-through molecules, such as aminoglycoside antibiotics, have been tested on mRNAs carrying premature stop codons. These findings have introduced new hopes for the development of a pharmacological approach to the β039 thalassemia therapy. While several strategies, designed to enhance translational read-through, have been reported to inhibit NMD efficiency concomitantly, experimental tools for systematic analysis of mammalian NMD inhibition by translational read-through are lacking. RESULTS We developed a human cellular model of the β039 thalassemia mutation with UPF-1 suppressed and showing a partial NMD suppression. CONCLUSIONS This novel cellular model could be used for the screening of molecules exhibiting preferential read-through activity allowing a great rescue of the mutated transcripts.
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Affiliation(s)
- Francesca Salvatori
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Mariangela Pappadà
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Giulia Breveglieri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.,Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Elisabetta D'Aversa
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy. .,Biotechnology Center, University of Ferrara, Ferrara, Italy.
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.
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13
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Optimized approach for the identification of highly efficient correctors of nonsense mutations in human diseases. PLoS One 2017; 12:e0187930. [PMID: 29131862 PMCID: PMC5683606 DOI: 10.1371/journal.pone.0187930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
About 10% of patients with a genetic disease carry a nonsense mutation causing their pathology. A strategy for correcting nonsense mutations is premature termination codon (PTC) readthrough, i.e. incorporation of an amino acid at the PTC position during translation. PTC-readthrough-activating molecules appear as promising therapeutic tools for these patients. Unfortunately, the molecules shown to induce PTC readthrough show low efficacy, probably because the mRNAs carrying a nonsense mutation are scarce, as they are also substrates of the quality control mechanism called nonsense-mediated mRNA decay (NMD). The screening systems previously developed to identify readthrough-promoting molecules used cDNA constructs encoding mRNAs immune to NMD. As the molecules identified were not selected for the ability to correct nonsense mutations on NMD-prone PTC-mRNAs, they could be unsuitable for the context of nonsense-mutation-linked human pathologies. Here, a screening system based on an NMD-prone mRNA is described. It should be suitable for identifying molecules capable of efficiently rescuing the expression of human genes harboring a nonsense mutation. This system should favor the discovery of candidate drugs for treating genetic diseases caused by nonsense mutations. One hit selected with this screening system is presented and validated on cells from three cystic fibrosis patients.
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Azab B, Dardas Z, Hamarsheh M, Alsalem M, Kilani Z, Kilani F, Awidi A, Jafar H, Amr S. Novel frameshift variant in the IDUA gene underlies Mucopolysaccharidoses type I in a consanguineous Yemeni pedigree. Mol Genet Metab Rep 2017. [PMID: 28649516 PMCID: PMC5470527 DOI: 10.1016/j.ymgmr.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS I) is an autosomal recessive storage disorder that result as a consequence of a deficiency in the lysosomal hydrolase, a-L-iduronidase enzyme encoded by IDUA gene. Over a hundred causative variants in IDUA have been identified, which result in a progressive multi-systemic disease with a broad range of severity and disease progression reported across affected individuals. The aim of this study was the detection and interpretation of IDUA mutation in a family with two children affected with lethal MPS I. The IDUA gene was sequenced in the parents of two deceased children who had a clinical diagnosis of MPS I, to assess their carrier status and to help inform on risk in future children. The sequencing analysis was performed by PCR and bidirectional Sanger sequencing of the coding region and exon-intron splice junctions at Labor MVZ Westmecklenburg molecular diagnostics laboratory. A heterozygous c.657delA variant in exon 6 was identified in each parent, which is the most likely explanation for disease in their children. This report represents the first Yemeni family to have a molecular diagnosis for MPS I.
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Affiliation(s)
- Belal Azab
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan.,Department of Medical Laboratory Sciences, School of Science, The University of Jordan, Amman 11942, Jordan.,Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Zain Dardas
- Department of Medical Laboratory Sciences, School of Science, The University of Jordan, Amman 11942, Jordan.,Cell Therapy Center, The University of Jordan, Amman 11942, Jordan.,Department of Medical Laboratory Sciences, Faculty of Applied Medical sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | | | - Mohammad Alsalem
- Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | | | | | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan.,Department of Internal Medicine Hematology and Oncology Unit, The University of Jordan, Amman 11942, Jordan
| | - Hanan Jafar
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Sami Amr
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, USA
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