1
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Tocchini C, Mango SE. An adapted MS2-MCP system to visualize endogenous cytoplasmic mRNA with live imaging in Caenorhabditis elegans. PLoS Biol 2024; 22:e3002526. [PMID: 38427703 PMCID: PMC10936773 DOI: 10.1371/journal.pbio.3002526] [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: 08/07/2023] [Revised: 03/13/2024] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
Live imaging of RNA molecules constitutes an invaluable means to track the dynamics of mRNAs, but live imaging in Caenorhabditis elegans has been difficult to achieve. Endogenous transcripts have been observed in nuclei, but endogenous mRNAs have not been detected in the cytoplasm, and functional mRNAs have not been generated. Here, we have adapted live imaging methods to visualize mRNA in embryonic cells. We have tagged endogenous transcripts with MS2 hairpins in the 3' untranslated region (UTR) and visualized them after adjusting MS2 Coat Protein (MCP) expression. A reduced number of these transcripts accumulates in the cytoplasm, leading to loss-of-function phenotypes. In addition, during epithelial morphogenesis, MS2-tagged mRNAs for dlg-1 fail to associate with the adherens junction, as observed for untagged, endogenous mRNAs. These defects are reversed by inactivating the nonsense-mediated decay pathway. RNA accumulates in the cytoplasm, mutant phenotypes are rescued, and dlg-1 RNA associates with the adherens junction. These data suggest that MS2 repeats can induce the degradation of endogenous RNAs and alter their cytoplasmic distribution. Although our focus is RNAs expressed in epithelial cells during morphogenesis, we find that this method can be applied to other cell types and stages.
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2
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Zheng Z, Song Y, Tan X. Deciphering hERG Mutation in Long QT Syndrome Type 2 Using Antisense Oligonucleotide-Mediated Techniques: Lessons from Cystic Fibrosis. Heart Rhythm 2023:S1547-5271(23)02180-X. [PMID: 37121422 DOI: 10.1016/j.hrthm.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/02/2023]
Abstract
Long QT syndrome type 2 (LQT2) is a genetic disorder caused by mutations in the KCNH2 gene, also known as the human ether-a-go-go-related gene (hERG). Over 30% of hERG mutations result in a premature termination codon (PTC) that triggers a process called nonsense-mediated mRNA decay (NMD), where the mRNA transcript is degraded. NMD is a quality control mechanism that removes faulty mRNA to prevent the translation of truncated proteins. Recent advances in antisense oligonucleotide (ASO) technology in the field of cystic fibrosis (CF) have yielded significant progress, including the ASO-mediated comprehensive characterization of key NMD factors and exon-skipping therapy. These advances have contributed to our understanding of the role of PTC-containing mutations in disease phenotypes and have also led to the development of potentially useful therapeutic strategies. Historically, studies of CF have provided valuable insights for the research on LQT2, particularly concerning increasing the expression of hERG. In this article, we outline the current state of knowledge regarding ASO, NMD, and hERG and discuss the introduction of ASO technology in the CF to elucidate the pathogenic mechanisms through targeting NMD. We also discuss the potential clinical therapeutic benefits and limitations of ASO for the management of LQT2. By drawing on lessons learned from CF research, we explore the potential translational values of these advances into LQT2 studies.
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Affiliation(s)
- Zequn Zheng
- Department of Cardiology, Shantou University Medical College, Shantou, China; Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, China; Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, China.
| | - Yongfei Song
- Ningbo Institute for Medicine &Biomedical Engineering Combined Innovation, Ningbo, China
| | - Xuerui Tan
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, China; Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, China.
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3
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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4
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Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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5
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Sanderlin EJ, Keenan MM, Mense M, Revenko AS, Monia BP, Guo S, Huang L. CFTR mRNAs with nonsense codons are degraded by the SMG6-mediated endonucleolytic decay pathway. Nat Commun 2022; 13:2344. [PMID: 35487895 PMCID: PMC9054838 DOI: 10.1038/s41467-022-29935-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/24/2022] [Indexed: 12/22/2022] Open
Abstract
Approximately 10% of cystic fibrosis patients harbor nonsense mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene which can generate nonsense codons in the CFTR mRNA and subsequently activate the nonsense-mediated decay (NMD) pathway resulting in rapid mRNA degradation. However, it is not known which NMD branches govern the decay of CFTR mRNAs containing nonsense codons. Here we utilize antisense oligonucleotides targeting NMD factors to evaluate the regulation of nonsense codon-containing CFTR mRNAs by the NMD pathway. We observe that CFTR mRNAs with nonsense codons G542X, R1162X, and W1282X, but not Y122X, require UPF2 and UPF3 for NMD. Furthermore, we demonstrate that all evaluated CFTR mRNAs harboring nonsense codons are degraded by the SMG6-mediated endonucleolytic pathway rather than the SMG5-SMG7-mediated exonucleolytic pathway. Finally, we show that upregulation of all evaluated CFTR mRNAs with nonsense codons by NMD pathway inhibition improves outcomes of translational readthrough therapy.
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Affiliation(s)
| | | | - Martin Mense
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | | | | | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Lulu Huang
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA.
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6
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Li D, Liu Y, Yi P, Zhu Z, Li W, Zhang QC, Li JB, Ou G. RNA editing restricts hyperactive ciliary kinases. Science 2021; 373:984-991. [PMID: 34446600 DOI: 10.1126/science.abd8971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Protein kinase activity must be precisely regulated, but how a cell governs hyperactive kinases remains unclear. In this study, we generated a constitutively active mitogen-activated protein kinase DYF-5 (DYF-5CA) in Caenorhabditis elegans that disrupted sensory cilia. Genetic suppressor screens identified that mutations of ADR-2, an RNA adenosine deaminase, rescued ciliary phenotypes of dyf-5CA We found that dyf-5CA animals abnormally transcribed antisense RNAs that pair with dyf-5CA messenger RNA (mRNA) to form double-stranded RNA, recruiting ADR-2 to edit the region ectopically. RNA editing impaired dyf-5CA mRNA splicing, and the resultant intron retentions blocked DYF-5CA protein translation and activated nonsense-mediated dyf-5CA mRNA decay. The kinase RNA editing requires kinase hyperactivity. The similar RNA editing-dependent feedback regulation restricted the other ciliary kinases NEKL-4/NEK10 and DYF-18/CCRK, which suggests a widespread mechanism that underlies kinase regulation.
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Affiliation(s)
- Dongdong Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Yufan Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Peishan Yi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China. .,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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7
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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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8
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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9
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Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes. Int J Mol Sci 2020; 21:ijms21134672. [PMID: 32630050 PMCID: PMC7369780 DOI: 10.3390/ijms21134672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman–Diamond syndrome (SDS), Diamond–Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.
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10
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Lindeboom RGH, Vermeulen M, Lehner B, Supek F. The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. Nat Genet 2019; 51:1645-1651. [PMID: 31659324 PMCID: PMC6858879 DOI: 10.1038/s41588-019-0517-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022]
Abstract
Premature termination codons (PTCs) can result in the production of truncated proteins or the degradation of messenger RNAs by nonsense-mediated mRNA decay (NMD). Which of these outcomes occurs can alter the effect of a mutation, with the engagement of NMD being dependent on a series of rules. Here, by applying these rules genome-wide to obtain a resource called NMDetective, we explore the impact of NMD on genetic disease and approaches to therapy. First, human genetic diseases differ in whether NMD typically aggravates or alleviates the effects of PTCs. Second, failure to trigger NMD is a cause of ineffective gene inactivation by CRISPR-Cas9 gene editing. Finally, NMD is a determinant of the efficacy of cancer immunotherapy, with only frameshifted transcripts that escape NMD predicting a response. These results demonstrate the importance of incorporating the rules of NMD into clinical decision-making. Moreover, they suggest that inhibiting NMD may be effective in enhancing cancer immunotherapy.
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Affiliation(s)
- Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| | - Fran Supek
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain. .,Institut de Recerca Biomedica Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
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11
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Ahrens-Nicklas RC, Pappas CT, Farman GP, Mayfield RM, Larrinaga TM, Medne L, Ritter A, Krantz ID, Murali C, Lin KY, Berger JH, Yum SW, Carreon CK, Gregorio CC. Disruption of cardiac thin filament assembly arising from a mutation in LMOD2: A novel mechanism of neonatal dilated cardiomyopathy. SCIENCE ADVANCES 2019; 5:eaax2066. [PMID: 31517052 PMCID: PMC6726455 DOI: 10.1126/sciadv.aax2066] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/31/2019] [Indexed: 05/10/2023]
Abstract
Neonatal heart failure is a rare, poorly-understood presentation of familial dilated cardiomyopathy (DCM). Exome sequencing in a neonate with severe DCM revealed a homozygous nonsense variant in leiomodin 2 (LMOD2, p.Trp398*). Leiomodins (Lmods) are actin-binding proteins that regulate actin filament assembly. While disease-causing mutations in smooth (LMOD1) and skeletal (LMOD3) muscle isoforms have been described, the cardiac (LMOD2) isoform has not been previously associated with human disease. Like our patient, Lmod2-null mice have severe early-onset DCM and die before weaning. The infant's explanted heart showed extraordinarily short thin filaments with isolated cardiomyocytes displaying a large reduction in maximum calcium-activated force production. The lack of extracardiac symptoms in Lmod2-null mice, and remarkable morphological and functional similarities between the patient and mouse model informed the decision to pursue cardiac transplantation in the patient. To our knowledge, this is the first report of aberrant cardiac thin filament assembly associated with human cardiomyopathy.
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Affiliation(s)
- Rebecca C. Ahrens-Nicklas
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher T. Pappas
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Gerrie P. Farman
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Rachel M. Mayfield
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Tania M. Larrinaga
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Livija Medne
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Alyssa Ritter
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ian D. Krantz
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chaya Murali
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kimberly Y. Lin
- Division of Pediatric Cardiology, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Justin H. Berger
- Division of Pediatric Cardiology, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sabrina W. Yum
- Division of Pediatric Neurology, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chrystalle Katte Carreon
- Department of Pathology, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
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12
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Usuki F, Yamashita A, Fujimura M. Environmental stresses suppress nonsense-mediated mRNA decay (NMD) and affect cells by stabilizing NMD-targeted gene expression. Sci Rep 2019; 9:1279. [PMID: 30718659 PMCID: PMC6362056 DOI: 10.1038/s41598-018-38015-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular mechanism that eliminates mRNAs that harbor premature translation termination codons (PTCs). Here, we investigated the effects of environmental stresses (oxidative stress and endoplasmic reticulum (ER) stress) on NMD activity. Methylmercury (MeHg) was used to cause oxidative stress and thapsigargin to stress the ER. NMD suppression, evidenced by upregulation of NMD-sensitive mRNAs and a decrease in UPF1 phosphorylation, was observed in MeHg-treated myogenic cells, cerebral cortical neuronal cells, and astroglial cells. Mild ER stress amplified NMD suppression caused by MeHg. To elucidate the cause of stress-induced NMD suppression, the role of the phospho-eIF2α/ATF4 pathway was investigated. Knockdown and non-phosphorylatable eIF2α-transfection studies demonstrated the critical role of phospho-eIF2α-mediated repression of translation in mild ER stress-induced NMD suppression. However, NMD suppression was also observed in phospho-eIF2α-deficient cells under mild ER stress. Mechanistic target of rapamycin suppression-induced inhibition of cap-dependent translation, and downregulation of the NMD components UPF1, SMG7, and eIF4A3, were probably involved in stress-induced NMD suppression. Our results indicate that stress-induced NMD suppression has the potential to affect the condition of cells and phenotypes of PTC-related diseases under environmental stresses by stabilizing NMD-targeted gene expression.
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Affiliation(s)
- Fusako Usuki
- Department of Clinical Medicine, National Institute for Minamata Disease, 4058-18 Hama, Minamata, 867-0008, Japan.
| | - Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, 3-9 Fuku-ura, Kanazawa, Yokohama, 236-0004, Japan
| | - Masatake Fujimura
- Basic Medical Sciences, National Institute for Minamata Disease, 4058-18 Hama, Minamata, 867-0008, Japan
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13
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Huang L, Low A, Damle SS, Keenan MM, Kuntz S, Murray SF, Monia BP, Guo S. Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations. Genome Biol 2018; 19:4. [PMID: 29334995 PMCID: PMC5769327 DOI: 10.1186/s13059-017-1386-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/29/2017] [Indexed: 01/08/2023] Open
Abstract
Background About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncated proteins, but also often result in decreased mRNA abundance due to nonsense-mediated mRNA decay (NMD). Although pharmacological inhibition of NMD could be an attractive therapeutic approach for the treatment of diseases caused by nonsense mutations, NMD also regulates the expression of 10–20% of the normal transcriptome. Results Here, we investigate whether NMD can be inhibited to stabilize mutant mRNAs, which may subsequently produce functional proteins, without having a major impact on the normal transcriptome. We develop antisense oligonucleotides (ASOs) to systematically deplete each component in the NMD pathway. We find that ASO-mediated depletion of each NMD factor elicits different magnitudes of NMD inhibition in vitro and are differentially tolerated in normal mice. Among all of the NMD factors, Upf3b depletion is well tolerated, consistent with previous reports that UPF3B is not essential for development and regulates only a subset of the endogenous NMD substrates. While minimally impacting the normal transcriptome, Upf3b-ASO treatment significantly stabilizes the PTC-containing dystrophin mRNA in mdx mice and coagulation factor IX mRNA in a hemophilia mouse model. Furthermore, when combined with reagents promoting translational read-through, Upf3b-ASO treatment leads to the production of functional factor IX protein in hemophilia mice. Conclusions These data demonstrate that ASO-mediated reduction of the NMD factor Upf3b could be an effective and safe approach for the treatment of diseases caused by nonsense mutations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1386-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lulu Huang
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Audrey Low
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Sagar S Damle
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | - Steven Kuntz
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | - Brett P Monia
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA.
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14
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Usuki F, Fujimura M, Yamashita A. Endoplasmic reticulum stress preconditioning modifies intracellular mercury content by upregulating membrane transporters. Sci Rep 2017; 7:12390. [PMID: 28959040 PMCID: PMC5620048 DOI: 10.1038/s41598-017-09435-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/27/2017] [Indexed: 01/02/2023] Open
Abstract
Endoplasmic reticulum (ER) stress preconditioning protects cells against methylmercury (MeHg) cytotoxicity by inducing integrated stress responses such as eIF2α phosphorylation, ATF4 accumulation, and nonsense-mediated mRNA decay (NMD) suppression. Here we demonstrated that ER stress preconditioning results in the upregulation of membrane transporters, leading to a decrease in intracellular mercury content. Our analyses showed that ER stress preconditioning upregulated the expression of methionine transporters that affect the cellular influx of MeHg, LAT1, LAT3, and SNAT2; and a membrane transporter that affects the efflux of MeHg, ABCC4, in MeHg-susceptible myogenic cells. Among these, ABCC4 transporter expression exhibited the greatest elevation. The functional significance of ABCC4 transporter in the efflux of MeHg was shown by the ABCC4 inhibition study. Additionally, we identified the role of phospho-eIF2α/ATF4 pathway in the upregulation of LAT1, SNAT2, and ABCC4 and the role of NMD suppression in LAT3 upregulation. Further, we detected that ER stress preconditioning amplified membrane transporter expression most likely through the translation of the upregulated mRNAs caused by ATF4-dependent transcription and NMD suppression. Taken together, these results suggested that the phospho-eIF2α/ATF4 pathway activation and NMD suppression may represent therapeutic targets for the alleviation of MeHg cytotoxicity by enhancing mercury efflux besides inducing protective stress responses.
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Affiliation(s)
- Fusako Usuki
- Department of Clinical Medicine, National Institute for Minamata Disease, Kumamoto, 867-0008, Japan.
| | - Masatake Fujimura
- Department of Basic Medical Sciences, National Institute for Minamata Disease, Kumamoto, 867-0008, Japan
| | - Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
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15
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Li L, Lingaraju M, Basquin C, Basquin J, Conti E. Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA (NEW YORK, N.Y.) 2017; 23:1028-1034. [PMID: 28389433 PMCID: PMC5473137 DOI: 10.1261/rna.061200.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans We found that SMG8-SMG9 is a G-domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1. The SMG8-SMG9 heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans. Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. Fitting the GDP-bound SMG8-SMG9 structure in EM densities of the human SMG1-SMG8-SMG9 complex raises the possibility that the nucleotide site of SMG9 faces SMG1 and could impact the kinase conformation and/or regulation.
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Affiliation(s)
- Liang Li
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Jérome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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16
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Hsu MK, Lin HY, Chen FC. NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events. PLoS One 2017; 12:e0174798. [PMID: 28369084 PMCID: PMC5378362 DOI: 10.1371/journal.pone.0174798] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/15/2017] [Indexed: 01/23/2023] Open
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation–an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
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Affiliation(s)
- Min-Kung Hsu
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
| | - Hsuan-Yu Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
| | - Feng-Chi Chen
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
- School of Dentistry, China Medical University, Taichung City, Taiwan
- * E-mail:
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17
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Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Mol Cell 2017; 65:191-201. [PMID: 28017590 PMCID: PMC5301997 DOI: 10.1016/j.molcel.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/05/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs containing a premature termination codon (PTC). PTCs are a frequent cause of human genetic diseases, and the NMD pathway is known to modulate disease severity. Since partial NMD attenuation can potentially enhance nonsense suppression therapies, better definition of human-specific NMD is required. However, the majority of NMD factors were first discovered in model organisms and then subsequently identified by homology in human. Sensitivity and throughput limitations of existing approaches have hindered systematic forward genetic screening for NMD factors in human cells. We developed a method of in vivo amplification of NMD reporter fluorescence (Fireworks) that enables CRISPR-based forward genetic screening for NMD pathway defects in human cells. The Fireworks genetic screen identifies multiple known NMD factors and numerous human candidate genes, providing a platform for discovery of additional key factors in human mRNA degradation.
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Affiliation(s)
- Andrei Alexandrov
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
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18
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Deniaud A, Karuppasamy M, Bock T, Masiulis S, Huard K, Garzoni F, Kerschgens K, Hentze MW, Kulozik AE, Beck M, Neu-Yilik G, Schaffitzel C. A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation. Nucleic Acids Res 2015; 43:7600-11. [PMID: 26130714 PMCID: PMC4551919 DOI: 10.1093/nar/gkv668] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/18/2015] [Indexed: 01/09/2023] Open
Abstract
Mammalian nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that degrades mRNAs containing premature translation termination codons. Phosphorylation of the essential NMD effector UPF1 by the phosphoinositide-3-kinase-like kinase (PIKK) SMG-1 is a key step in NMD and occurs when SMG-1, its two regulatory factors SMG-8 and SMG-9, and UPF1 form a complex at a terminating ribosome. Electron cryo-microscopy of the SMG-1–8–9-UPF1 complex shows the head and arm architecture characteristic of PIKKs and reveals different states of UPF1 docking. UPF1 is recruited to the SMG-1 kinase domain and C-terminal insertion domain, inducing an opening of the head domain that provides access to the active site. SMG-8 and SMG-9 interact with the SMG-1 C-insertion and promote high-affinity UPF1 binding to SMG-1–8–9, as well as decelerated SMG-1 kinase activity and enhanced stringency of phosphorylation site selection. The presence of UPF2 destabilizes the SMG-1–8–9-UPF1 complex leading to substrate release. Our results suggest an intricate molecular network of SMG-8, SMG-9 and the SMG-1 C-insertion domain that governs UPF1 substrate recruitment and phosphorylation by SMG-1 kinase, an event that is central to trigger mRNA decay.
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Affiliation(s)
- Aurélien Deniaud
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Simonas Masiulis
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Karine Huard
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frédéric Garzoni
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Kathrin Kerschgens
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble, France School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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19
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Yonekawa T, Nishino I. Ullrich congenital muscular dystrophy: clinicopathological features, natural history and pathomechanism(s). J Neurol Neurosurg Psychiatry 2015; 86:280-7. [PMID: 24938411 DOI: 10.1136/jnnp-2013-307052] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Collagen VI is widely distributed throughout extracellular matrices (ECMs) in various tissues. In skeletal muscle, collagen VI is particularly concentrated in and adjacent to basement membranes of myofibers. Ullrich congenital muscular dystrophy (UCMD) is caused by mutations in either COL6A1, COL6A2 or COL6A3 gene, thereby leading to collagen VI deficiency in the ECM. It is known to occur through either recessive or dominant genetic mechanism, the latter most typically by de novo mutations. UCMD is well defined by the clinicopathological hallmarks including distal hyperlaxity, proximal joint contractures, protruding calcanei, scoliosis and respiratory insufficiency. Recent reports have depicted the robust natural history of UCMD; that is, loss of ambulation by early teenage years, rapid decline in respiratory function by 10 years of age and early-onset, rapidly progressive scoliosis. Muscle pathology is characterised by prominent interstitial fibrosis disproportionate to the relative paucity of necrotic and regenerating fibres. To date, treatment for patients is supportive for symptoms such as joint contractures, respiratory failure and scoliosis. There have been clinical trials based on the theory of mitochondrion-mediated myofiber apoptosis or impaired autophagy. Furthermore, the fact that collagen VI producing cells in skeletal muscle are interstitial mesenchymal cells can support proof of concept for stem cell-based therapy.
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Affiliation(s)
- Takahiro Yonekawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan Department of Child Neurology, National Center Hospital, NCNP, Kodaira, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan Department of Clinical Development, Translational Medical Center, NCNP
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20
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A computational strategy to select optimized protein targets for drug development toward the control of cancer diseases. PLoS One 2015; 10:e0115054. [PMID: 25625699 PMCID: PMC4308075 DOI: 10.1371/journal.pone.0115054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/21/2014] [Indexed: 12/18/2022] Open
Abstract
In this report, we describe a strategy for the optimized selection of protein targets suitable for drug development against neoplastic diseases taking the particular case of breast cancer as an example. We combined human interactome and transcriptome data from malignant and control cell lines because highly connected proteins that are up-regulated in malignant cell lines are expected to be suitable protein targets for chemotherapy with a lower rate of undesirable side effects. We normalized transcriptome data and applied a statistic treatment to objectively extract the sub-networks of down- and up-regulated genes whose proteins effectively interact. We chose the most connected ones that act as protein hubs, most being in the signaling network. We show that the protein targets effectively identified by the combination of protein connectivity and differential expression are known as suitable targets for the successful chemotherapy of breast cancer. Interestingly, we found additional proteins, not generally targeted by drug treatments, which might justify the extension of existing formulation by addition of inhibitors designed against these proteins with the consequence of improving therapeutic outcomes. The molecular alterations observed in breast cancer cell lines represent either driver events and/or driver pathways that are necessary for breast cancer development or progression. However, it is clear that signaling mechanisms of the luminal A, B and triple negative subtypes are different. Furthermore, the up- and down-regulated networks predicted subtype-specific drug targets and possible compensation circuits between up- and down-regulated genes. We believe these results may have significant clinical implications in the personalized treatment of cancer patients allowing an objective approach to the recycling of the arsenal of available drugs to the specific case of each breast cancer given their distinct qualitative and quantitative molecular traits.
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21
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Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014; 16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA structures (ARSs), or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs) and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s) into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan.
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22
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Nozaki H, Nishizawa M, Onodera O. Features of cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy. Stroke 2014; 45:3447-53. [PMID: 25116877 DOI: 10.1161/strokeaha.114.004236] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroaki Nozaki
- From the Department of Medical Technology, School of Health Sciences Faculty of Medicine (H.N.), Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute (M.N.), and Department of Molecular Neuroscience, Resource Branch for Brain Disease, Brain Research Institute (O.O.), Niigata University, Niigata, Japan
| | - Masatoyo Nishizawa
- From the Department of Medical Technology, School of Health Sciences Faculty of Medicine (H.N.), Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute (M.N.), and Department of Molecular Neuroscience, Resource Branch for Brain Disease, Brain Research Institute (O.O.), Niigata University, Niigata, Japan
| | - Osamu Onodera
- From the Department of Medical Technology, School of Health Sciences Faculty of Medicine (H.N.), Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute (M.N.), and Department of Molecular Neuroscience, Resource Branch for Brain Disease, Brain Research Institute (O.O.), Niigata University, Niigata, Japan.
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23
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Seyedali A, Berry MJ. Nonsense-mediated decay factors are involved in the regulation of selenoprotein mRNA levels during selenium deficiency. RNA (NEW YORK, N.Y.) 2014; 20:1248-1256. [PMID: 24947499 PMCID: PMC4105750 DOI: 10.1261/rna.043463.113] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
Selenoproteins contain the unique amino acid selenocysteine (Sec), which is encoded by the triplet UGA. Since UGA also serves as a stop codon, it has been postulated that selenoprotein mRNAs are targeted for degradation by the nonsense-mediated mRNA decay pathway (NMD). Several reports have observed a hierarchy of selenoprotein mRNA expression when selenium (Se) is limiting, whereby the abundance of certain transcripts decline while others do not. We sought to investigate the role of NMD in this hierarchical response that selenoprotein mRNAs exhibit to environmental Se status. Selenoprotein mRNAs were categorized as being predicted sensitive or resistant to NMD based on the requirements held by the current model. About half of the selenoprotein transcriptome was predicted to be sensitive to NMD and showed significant changes in mRNA abundance in response to cellular Se status. The other half that was predicted to be resistant to NMD did not respond to Se status. RNA immunoprecipitation with essential NMD factor UPF1 revealed that the mRNAs that were the most sensitive to Se status were also the most enriched on UPF1 during Se deficiency. Furthermore, depletion of SMG1, the kinase responsible for UPF1 phosphorylation and NMD activation, abrogated the decline in transcript abundance of Se-responsive transcripts. Lastly, mRNA decay rates of Se-responsive transcripts were altered upon the addition of Se to resemble the slower decay rates of nonresponsive transcripts. Taken together, these results present novel evidence in support of a crucial role for the NMD pathway in regulating selenoprotein mRNA levels when Se is limiting.
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Affiliation(s)
- Ali Seyedali
- Department of Cell and Molecular Biology, John A. Burn School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Marla J Berry
- Department of Cell and Molecular Biology, John A. Burn School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
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24
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Melero R, Uchiyama A, Castaño R, Kataoka N, Kurosawa H, Ohno S, Yamashita A, Llorca O. Structures of SMG1-UPFs complexes: SMG1 contributes to regulate UPF2-dependent activation of UPF1 in NMD. Structure 2014; 22:1105-1119. [PMID: 25002321 DOI: 10.1016/j.str.2014.05.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 12/31/2022]
Abstract
SMG1, a PI3K-related kinase, plays a critical role in nonsense-mediated mRNA decay (NMD) in mammals. SMG1-mediated phosphorylation of the UPF1 helicase is an essential step during NMD initiation. Both SMG1 and UPF1 are presumably activated by UPF2, but this regulation is incompletely understood. Here we reveal that SMG1C (a complex containing SMG1, SMG8, and SMG9) contributes to regulate NMD by recruiting UPF1 and UPF2 to distinct sites in the vicinity of the kinase domain. UPF2 binds SMG1 in an UPF1-independent manner in vivo, and the SMG1C-UPF2 structure shows UPF2 recognizes the FRB domain, a region that regulates the related mTOR kinase. The molecular architectures of several SMG1C-UPFs complexes, obtained by combining electron microscopy with in vivo and in vitro interaction analyses, competition experiments, and mutations, suggest that UPF2 can be transferred to UPF1 within SMG1C, inducing UPF2-dependent conformational changes required to activate UPF1 within an SMG1C-UPF1-UPF2 complex.
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Affiliation(s)
- Roberto Melero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Akiko Uchiyama
- Department of Molecular Biology, Yokohama City University School of Medicine, 3-9, Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Raquel Castaño
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Naoyuki Kataoka
- Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, 53, Shogoin Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hitomi Kurosawa
- Department of Molecular Biology, Yokohama City University School of Medicine, 3-9, Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, 3-9, Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, 3-9, Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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25
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Abstract
Nonsense suppression therapy encompasses approaches aimed at suppressing translation termination at in-frame premature termination codons (PTCs, also known as nonsense mutations) to restore deficient protein function. In this review, we examine the current status of PTC suppression as a therapy for genetic diseases caused by nonsense mutations. We discuss what is currently known about the mechanism of PTC suppression as well as therapeutic approaches under development to suppress PTCs. The approaches considered include readthrough drugs, suppressor tRNAs, PTC pseudouridylation, and inhibition of nonsense-mediated mRNA decay. We also discuss the barriers that currently limit the clinical application of nonsense suppression therapy and suggest how some of these difficulties may be overcome. Finally, we consider how PTC suppression may play a role in the clinical treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology and Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama 35294; , , ,
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