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Zhao C, Liu Y, Zhang P, Xia X, Yang Y. Alternative splicing plays a nonredundant role in greater amberjack (Seriola dumerili) in acclimation to ambient salinity fluctuations. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106549. [PMID: 38733739 DOI: 10.1016/j.marenvres.2024.106549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
Alternative splicing (AS) is an important post-transcriptional mechanism for adaptation of fish to environmental stress. Here, we performed a genome-wide investigation to AS dynamics in greater amberjack (Seriola dumerili), an economical marine teleost, in response to hypo- (10 ppt) and hyper-salinity (40 ppt) stresses. Totally, 2267-2611 differentially spliced events were identified in gills and kidney upon the exposure to undesired salinity regimes. In gills, genes involved in energy metabolism, stimulus response and epithelial cell differentiation were differentially spliced in response to salinity variation, while sodium ion transport and cellular amide metabolism were enhanced in kidney to combat the adverse impacts of salinity changes. Most of these differentially spliced genes were not differentially expressed, and AS was found to regulate different biological processes from differential gene expression, indicative of the functionally nonredundant role of AS in modulating salinity acclimation in greater amberjack. Together, our study highlights the important contribution of post-transcriptional mechanisms to the adaptation of fish to ambient salinity fluctuations and provides theoretical guidance for the conservation of marine fishery resources against increasingly environmental challenges.
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Affiliation(s)
- Chunyu Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Panpan Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Xinhui Xia
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
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2
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Ren Y, Luo X, Tong H, Wang S, Yan J, Lin L, Chen Y. Preliminary Study on Clinical Characteristics and Pathogenesis of IQSEC2 Mutations Patients. Pharmgenomics Pers Med 2024; 17:289-318. [PMID: 38827181 PMCID: PMC11144418 DOI: 10.2147/pgpm.s455840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/18/2024] [Indexed: 06/04/2024] Open
Abstract
Background The IQ motif and Sec7 domain ArfGEF 2 (IQSEC2), an X-linked gene that encodes the BRAG1 protein, is a guanine nucleotide exchange factor for the ADP ribosylation factor (ARF) protein family in the small guanosine triphosphate (GTP) binding protein. Mutations in this gene result in disorders such as intellectual disability (ID) and epilepsy. In this study, we analyze the clinical features of two patients with IQSEC2-mutation-related disease and discuss their possible pathogenesis. Methods The two patients were diagnosed with ID and epilepsy. Genetic testing was performed using whole-exome sequencing, and the three-dimensional protein structure was analyzed. UCSC Genome Browser was used to analyze the conservation of IQSEC2 in different species. We compared IQSEC2 expression in the proband families with that in a control group, as well as the expression of the postsynaptic identity protein 95 (PSD-95), synapse-associated protein 97 (SAP97), ADP ribosylation factor 6 (ARF-6), and insulin receptor substrate 53kDa (IRSP53) genes interacting with IQSEC2. Results We identified two semi-zygote mutations located in conserved positions in different species: an unreported de novo mutation, C.3576C>A (p. Tyr1192*), and a known mutation, c.2983C>T (p. Arg995Trp). IQSEC2 mutations resulted in significant changes in the predicted three-dimensional protein structure, while its expression in the two probands was significantly lower than that in the age-matched control group, and IQSEC2 expression in proband 1 was lower than that in his family members. The expression levels of PSD-95, ARF-6, and SAP97, IRSP 53, which interact with IQSEC2, were also significantly different from those in the family members and age-matched healthy children. Conclusion The clinical phenotype resulting from IQSEC2 mutations can be explained by the significant decrease in its expression, loss of function of the mutant protein, and change in the expression of related genes. Our results provide novel insights into the molecular phenotype conferred by the IQSEC2 variants.
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Affiliation(s)
- Yun Ren
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Xiaona Luo
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Haiyan Tong
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Simei Wang
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Jinbin Yan
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Longlong Lin
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
| | - Yucai Chen
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, People’s Republic of China
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Siddiqui A, Saxena A, Echols J, Havasi V, Fu L, Keeling KM. RNA binding proteins PTBP1 and HNRNPL regulate CFTR mRNA decay. Heliyon 2023; 9:e22281. [PMID: 38045134 PMCID: PMC10692906 DOI: 10.1016/j.heliyon.2023.e22281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
Background CFTR nonsense alleles generate negligible CFTR protein due to the nonsense mutation: 1) triggering CFTR mRNA degradation by nonsense-mediated mRNA decay (NMD), and 2) terminating CFTR mRNA translation prematurely. Thus, people with cystic fibrosis (PwCF) who carry nonsense alleles cannot benefit from current modulator drugs, which target CFTR protein. In this study, we examined whether PTBP1 and HNRNPL, two RNA binding proteins that protect a subset of mRNAs with a long 3' untranslated region (UTR) from NMD, similarly affect CFTR mRNA.Silencing RNAs were used to deplete PTBP1 or HNRNPL in 16HBE14o- human bronchial epithelial cells expressing WT, G542X, or W1282X CFTR. CFTR mRNA abundance was measured relative to controls by quantitative PCR. PTBP1 and HNRNPL were also exogenously expressed in each cell line and CFTR mRNA levels were similarly quantified. Results PTBP1 depletion reduced CFTR mRNA abundance in all three 16HBE14o- cell lines; HRNPL depletion reduced CFTR mRNA abundance in only the G542X and W1282X cell lines. Notably, decreased CFTR mRNA abundance correlated with increased mRNA decay. Exogenous expression of PTBP1 or HNRNPL increased CFTR mRNA abundance in all three cell lines; HNRNPL overexpression generally increased CFTR to a greater extent in G542X and W1282X 16HBE14o- cells.Our data indicate that PTBP1 and HNRNPL regulate CFTR mRNA abundance by protecting CFTR transcripts from NMD. This suggests that PTBP1 and/or HNRNPL may represent potential therapeutic targets to increase CFTR mRNA abundance and enhance responses to CFTR modulators and other therapeutic approaches in PwCF.
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Affiliation(s)
- Amna Siddiqui
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Comprehensive Cancer Center and, USA
| | - Arpit Saxena
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Joshua Echols
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Department of Pediatrics, Infectious Diseases Division, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Viktoria Havasi
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Comprehensive Cancer Center and, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
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Oliver KE, Carlon MS, Pedemonte N, Lopes-Pacheco M. The revolution of personalized pharmacotherapies for cystic fibrosis: what does the future hold? Expert Opin Pharmacother 2023; 24:1545-1565. [PMID: 37379072 PMCID: PMC10528905 DOI: 10.1080/14656566.2023.2230129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF), a potentially fatal genetic disease, is caused by loss-of-function mutations in the gene encoding for the CFTR chloride/bicarbonate channel. Modulator drugs rescuing mutant CFTR traffic and function are now in the clinic, providing unprecedented breakthrough therapies for people with CF (PwCF) carrying specific genotypes. However, several CFTR variants are unresponsive to these therapies. AREA COVERED We discussed several therapeutic approaches that are under development to tackle the fundamental cause of CF, including strategies targeting defective CFTR mRNA and/or protein expression and function. Alternatively, defective chloride secretion and dehydration in CF epithelia could be restored by exploiting pharmacological modulation of alternative targets, i.e., ion channels/transporters that concur with CFTR to maintain the airway surface liquid homeostasis (e.g., ENaC, TMEM16A, SLC26A4, SLC26A9, and ATP12A). Finally, we assessed progress and challenges in the development of gene-based therapies to replace or correct the mutant CFTR gene. EXPERT OPINION CFTR modulators are benefiting many PwCF responsive to these drugs, yielding substantial improvements in various clinical outcomes. Meanwhile, the CF therapy development pipeline continues to expand with the development of novel CFTR modulators and alternative therapeutic strategies with the ultimate goal of providing effective therapies for all PwCF in the foreseeable future.
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Affiliation(s)
- Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Marianne S. Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Ribeiro CMP, Higgs MG, Muhlebach MS, Wolfgang MC, Borgatti M, Lampronti I, Cabrini G. Revisiting Host-Pathogen Interactions in Cystic Fibrosis Lungs in the Era of CFTR Modulators. Int J Mol Sci 2023; 24:ijms24055010. [PMID: 36902441 PMCID: PMC10003689 DOI: 10.3390/ijms24055010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulators, a new series of therapeutics that correct and potentiate some classes of mutations of the CFTR, have provided a great therapeutic advantage to people with cystic fibrosis (pwCF). The main hindrances of the present CFTR modulators are related to their limitations in reducing chronic lung bacterial infection and inflammation, the main causes of pulmonary tissue damage and progressive respiratory insufficiency, particularly in adults with CF. Here, the most debated issues of the pulmonary bacterial infection and inflammatory processes in pwCF are revisited. Special attention is given to the mechanisms favoring the bacterial infection of pwCF, the progressive adaptation of Pseudomonas aeruginosa and its interplay with Staphylococcus aureus, the cross-talk among bacteria, the bronchial epithelial cells and the phagocytes of the host immune defenses. The most recent findings of the effect of CFTR modulators on bacterial infection and the inflammatory process are also presented to provide critical hints towards the identification of relevant therapeutic targets to overcome the respiratory pathology of pwCF.
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Affiliation(s)
- Carla M. P. Ribeiro
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (C.M.P.R.); (G.C.)
| | - Matthew G. Higgs
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marianne S. Muhlebach
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew C. Wolfgang
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Innthera4CF, Center on Innovative Therapies for Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Innthera4CF, Center on Innovative Therapies for Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
| | - Giulio Cabrini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Innthera4CF, Center on Innovative Therapies for Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: (C.M.P.R.); (G.C.)
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6
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Development of novel therapeutics for all individuals with CF (the future goes on). J Cyst Fibros 2023; 22 Suppl 1:S45-S49. [PMID: 36319570 DOI: 10.1016/j.jcf.2022.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/08/2022]
Abstract
Despite the major advances and successes in finding and establishing new treatments that tackle the basic defect in Cystic Fibrosis (CF), there is still an unmet need to bring these potentially curative therapies to all individuals with CF. Here, we review aspects of what is still missing to treat all individuals with CF by such approaches. On the one hand, we discuss novel holistic (high-throughput) approaches to elucidate mechanistic defects caused by distinct classes of mutations to identify novel drug targets. On the other hand, we examine therapeutic approaches to correct the gene in its own environment, i.e., in the genome.
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7
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Jackson JJ, Mao Y, White TR, Foye C, Oliver KE. Features of CFTR mRNA and implications for therapeutics development. Front Genet 2023; 14:1166529. [PMID: 37168508 PMCID: PMC10165737 DOI: 10.3389/fgene.2023.1166529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease impacting ∼100,000 people worldwide. This lethal disorder is caused by mutation of the CF transmembrane conductance regulator (CFTR) gene, which encodes an ATP-binding cassette-class C protein. More than 2,100 variants have been identified throughout the length of CFTR. These defects confer differing levels of severity in mRNA and/or protein synthesis, folding, gating, and turnover. Drug discovery efforts have resulted in recent development of modulator therapies that improve clinical outcomes for people living with CF. However, a significant portion of the CF population has demonstrated either no response and/or adverse reactions to small molecules. Additional therapeutic options are needed to restore underlying genetic defects for all patients, particularly individuals carrying rare or refractory CFTR variants. Concerted focus has been placed on rescuing variants that encode truncated CFTR protein, which also harbor abnormalities in mRNA synthesis and stability. The current mini-review provides an overview of CFTR mRNA features known to elicit functional consequences on final protein conformation and function, including considerations for RNA-directed therapies under investigation. Alternative exon usage in the 5'-untranslated region, polypyrimidine tracts, and other sequence elements that influence splicing are discussed. Additionally, we describe mechanisms of CFTR mRNA decay and post-transcriptional regulation mediated through interactions with the 3'-untranslated region (e.g. poly-uracil sequences, microRNAs). Contributions of synonymous single nucleotide polymorphisms to CFTR transcript utilization are also examined. Comprehensive understanding of CFTR RNA biology will be imperative for optimizing future therapeutic endeavors intended to address presently untreatable forms of CF.
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Affiliation(s)
- JaNise J. Jackson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Yiyang Mao
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Tyshawn R. White
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Catherine Foye
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
- *Correspondence: Kathryn E. Oliver,
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8
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Egan ME. Non-Modulator Therapies: Developing a Therapy for Every Cystic Fibrosis Patient. Clin Chest Med 2022; 43:717-725. [PMID: 36344076 DOI: 10.1016/j.ccm.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy brings hope to most patients with cystic fibrosis (CF), but not all. For approximately 12% of CF patients with premature termination codon mutations, large deletions, insertions, and frameshifts, the CFTR modulator therapy is not effective. Many believe that genetic-based therapies such as RNA therapies, DNA therapies, and gene editing technologies will be needed to treat mutations that are not responsive to modulator therapy. Delivery of these therapeutic agents to affected cells is the major challenge that will need to be overcome if we are to harness the power of these emerging therapies for the treatment of CF.
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Affiliation(s)
- Marie E Egan
- Division of Pulmonary Allergy Immunology Sleep Medicine, Department of Pediatrics, Pediatric Pulmonary Allergy Immunology and Sleep Medicine, Yale Cystic Fibrosis Center, School of Medicine, Yale University, 333 Cedar Street, PO Box 208064, New Haven, CT 06520, USA.
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9
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Kreda SM. Oligonucleotide-based therapies for cystic fibrosis. Curr Opin Pharmacol 2022; 66:102271. [PMID: 35988291 DOI: 10.1016/j.coph.2022.102271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
In the clinically successful era of CFTR modulators and Theratyping, 10-20% of individuals with cystic fibrosis (CF) may develop disease due to CFTR mutations that remain undruggable. These individuals produce low levels of CFTR mRNA and/or not enough protein to be rescued with modulator drugs. Alternative therapeutic approaches to correct the CFTR defect at the mRNA level using nucleic acid technologies are currently feasible; e.g., oligonucleotides platforms, which are being rapidly developed to correct genetic disorders. Drug-like properties, great specificity, and predictable off-target effects by design make oligonucleotides a valuable approach with fewer clinical and ethical challenges than genomic editing strategies. Together with personalized and precision medicine approaches, oligonucleotides are ideal therapeutics to target CF-causing mutations that affect only a few individuals resilient to modulator therapies.
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Affiliation(s)
- Silvia M Kreda
- Marsico Lung Institute / Cystic Fibrosis Center, University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill, NC, 27599-7248, USA; Department of Medicine, University of North Carolina at Chapel Hill, NC, 27599-7248, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, 27599-7248, USA.
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10
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Amaral MD. Precision medicine for rare diseases: The times they are A-Changin'. Curr Opin Pharmacol 2022; 63:102201. [DOI: 10.1016/j.coph.2022.102201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
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Gilbert A, Saveanu C. Unusual SMG suspects recruit degradation enzymes in nonsense-mediated mRNA decay. Bioessays 2022; 44:e2100296. [PMID: 35266563 DOI: 10.1002/bies.202100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Degradation of eukaryotic RNAs that contain premature termination codons (PTC) during nonsense-mediated mRNA decay (NMD) is initiated by RNA decapping or endonucleolytic cleavage driven by conserved factors. Models for NMD mechanisms, including recognition of PTCs or the timing and role of protein phosphorylation for RNA degradation are challenged by new results. For example, the depletion of the SMG5/7 heterodimer, thought to activate RNA degradation by decapping, leads to a phenotype showing a defect of endonucleolytic activity of NMD complexes. This phenotype is not correlated to a decreased binding of the endonuclease SMG6 with the core NMD factor UPF1, suggesting that it is the result of an imbalance between active (e.g., in polysomes) and inactive (e.g., in RNA-protein condensates) states of NMD complexes. Such imbalance between multiple complexes is not restricted to NMD and should be taken into account when establishing causal links between gene function perturbation and observed phenotypes.
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Affiliation(s)
- Agathe Gilbert
- Institut Pasteur, Sorbonne Université, CNRS UMR-3525, Paris, F-75015, France
| | - Cosmin Saveanu
- Institut Pasteur, Sorbonne Université, CNRS UMR-3525, Paris, F-75015, France
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12
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Guo M, Chen Y, Lin L, Wang Y, Wang A, Yuan F, Wang C, Wang S, Zhang Y. The Study on the Clinical Phenotype and Function of HPRT1 Gene. Child Neurol Open 2022; 9:2329048X221108821. [PMID: 35875183 PMCID: PMC9305801 DOI: 10.1177/2329048x221108821] [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: 05/07/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Lesch-Nyhan disease (LND) is a rare x-linked purine metabolic neurogenetic disease caused by enzyme hypoxanthine-guanine phosphoriribosyltransferase(HGprt) deficiency, also known as self-destructive appearance syndrome. A series of manifestations are caused by abnormal purine metabolism. The typical clinical manifestations are hyperuricemia, growth retardation, mental retardation, short stature, dance-like athetosis, aggressive behavior, and compulsive self-harm. Methods: We identified a point mutation c.151C > T (p. Arg51*) in a pedigree. We analyzed the clinical characteristics of children in a family, and obtained the blood of their parents and siblings for second-generation sequencing. At the same time, we also analyzed and compared the expression of HPRT1 gene and predicted the three-dimensional structure of the protein. And we analyzed the clinical manifestations caused by the defect of the HPRT1 gene. Results: The mutation led to the termination of transcription at the 51st arginine, resulting in the production of truncated protein, and the relative expression of HPRT1 gene in patients was significantly lower than other family members and 10 normal individuals. Conclusion: This mutation leads to the early termination of protein translation and the formation of a truncated HPRT protein, which affects the function of the protein and generates corresponding clinical manifestations.
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Affiliation(s)
- Miao Guo
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yucai Chen
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Longlong Lin
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yilin Wang
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Anqi Wang
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Yuan
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunmei Wang
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Simei Wang
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanfeng Zhang
- Department of Neurology, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai, China
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13
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Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021; 4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learning-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to validate the predictive analyses are defined, distinguishing between methods testing RNA (transcriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as suggestions on which approaches are more suitable in diagnostic rather than in clinical research.
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Affiliation(s)
| | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.)
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14
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Xie Z, Jiang J, Cao L, Jiang M, Yang F, Ma Z, Wang Z, Ruan C, Liu H, Zhou L. Nonsense-mediated mRNA decay efficiency influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) knock-in mice. Clin Genet 2021; 100:213-218. [PMID: 33928629 DOI: 10.1111/cge.13975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Glanzmann's thrombasthenia (GT) is a severe hemorrhagic disease. It is caused by mutations in ITGA2B or ITGB3, which are the respective genes encoding integrin αIIb and β3. Despite widespread mutational analysis, the mechanisms underlying the extensive variability in bleeding severity observed among affected individuals remains poorly understood. In order to explore the mechanisms conferring for bleeding heterogeneity, three GT patients with ITGA2B c.2671C > T (p.Q891X) who possessed different bleeding scores were studied. Analysis showed that there was significant difference in nonsense-mediated mRNA decay (NMD) efficiency among the three patients. These differences positively correlated with their bleeding score. Next, a knock-in mouse model (KI mice) with the ITGA2B c.2659C > T (p.Q887X) was generated using CRISPR/Cas9. Importantly, this mutation is homologous to ITGA2B c.2671C > T (p.Q891X) in humans. The bleeding time of KI mice was significantly in comparison to the wide-type mice. Interestingly, bleeding was stopped after treatment with caffeine, which is a known NMD inhibitor. This suggests that NMD efficiency potentially influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) KI mice.
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Affiliation(s)
- Zhanli Xie
- Department of Nuclear Medicine, Institute of Clinical Medicine Research, Suzhou Hospital (West District), Affiliated to Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, China
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiang Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Cao
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Miao Jiang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fei Yang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenni Ma
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhaoyue Wang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Liu
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Lu Zhou
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
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15
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Dang Y, van Heusden C, Nickerson V, Chung F, Wang Y, Quinney NL, Gentzsch M, Randell SH, Moulton HM, Kole R, Ni A, Juliano RL, Kreda SM. Enhanced delivery of peptide-morpholino oligonucleotides with a small molecule to correct splicing defects in the lung. Nucleic Acids Res 2021; 49:6100-6113. [PMID: 34107015 PMCID: PMC8216463 DOI: 10.1093/nar/gkab488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Pulmonary diseases offer many targets for oligonucleotide therapeutics. However, effective delivery of oligonucleotides to the lung is challenging. For example, splicing mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) affect a significant cohort of Cystic Fibrosis (CF) patients. These individuals could potentially benefit from treatment with splice switching oligonucleotides (SSOs) that can modulate splicing of CFTR and restore its activity. However, previous studies in cell culture used oligonucleotide transfection methods that cannot be safely translated in vivo. In this report, we demonstrate effective correction of a splicing mutation in the lung of a mouse model using SSOs. Moreover, we also demonstrate effective correction of a CFTR splicing mutation in a pre-clinical CF patient-derived cell model. We utilized a highly effective delivery strategy for oligonucleotides by combining peptide-morpholino (PPMO) SSOs with small molecules termed OECs. PPMOs distribute broadly into the lung and other tissues while OECs potentiate the effects of oligonucleotides by releasing them from endosomal entrapment. The combined PPMO plus OEC approach proved to be effective both in CF patient cells and in vivo in the mouse lung and thus may offer a path to the development of novel therapeutics for splicing mutations in CF and other lung diseases.
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Affiliation(s)
- Yan Dang
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Catharina van Heusden
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Veronica Nickerson
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Felicity Chung
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Yang Wang
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Nancy L Quinney
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Ryszard Kole
- Department of Pharmacology, The University of North Carolina at Chapel Hill, 4010 Genetic Medicine Bldg, Chapel Hill, NC 27599, USA
| | - Aiguo Ni
- Initos Pharmaceuticals, LLC, Chapel Hill, NC 27514, USA
| | | | - Silvia M Kreda
- Marsico Lung Institute/Cystic Fibrosis Center, The University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill NC 27599-7248, USA
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16
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He L, Kennedy AS, Houck S, Aleksandrov A, Quinney NL, Cyr-Scully A, Cholon DM, Gentzsch M, Randell SH, Ren HY, Cyr DM. DNAJB12 and Hsp70 triage arrested intermediates of N1303K-CFTR for endoplasmic reticulum-associated autophagy. Mol Biol Cell 2021; 32:538-553. [PMID: 33534640 PMCID: PMC8101465 DOI: 10.1091/mbc.e20-11-0688] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 11/11/2022] Open
Abstract
The transmembrane Hsp40 DNAJB12 and cytosolic Hsp70 cooperate on the endoplasmic reticulum's (ER) cytoplasmic face to facilitate the triage of nascent polytopic membrane proteins for folding versus degradation. N1303K is a common mutation that causes misfolding of the ion channel CFTR, but unlike F508del-CFTR, biogenic and functional defects in N1303K-CFTR are resistant to correction by folding modulators. N1303K is reported to arrest CFTR folding at a late stage after partial assembly of its N-terminal domains. N1303K-CFTR intermediates are clients of JB12-Hsp70 complexes, maintained in a detergent-soluble state, and have a relatively long 3-h half-life. ER-associated degradation (ERAD)-resistant pools of N1303K-CFTR are concentrated in ER tubules that associate with autophagy initiation sites containing WIPI1, FlP200, and LC3. Destabilization of N1303K-CFTR or depletion of JB12 prevents entry of N1303K-CFTR into the membranes of ER-connected phagophores and traffic to autolysosomes. In contrast, the stabilization of intermediates with the modulator VX-809 promotes the association of N1303K-CFTR with autophagy initiation machinery. N1303K-CFTR is excluded from the ER-exit sites, and its passage from the ER to autolysosomes does not require ER-phagy receptors. DNAJB12 operates in biosynthetically active ER microdomains to triage membrane protein intermediates in a conformation-specific manner for secretion versus degradation via ERAD or selective-ER-associated autophagy.
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Affiliation(s)
- Lihua He
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew S. Kennedy
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott Houck
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrei Aleksandrov
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nancy L. Quinney
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Alexandra Cyr-Scully
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Deborah M. Cholon
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Martina Gentzsch
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott H. Randell
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hong Yu Ren
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Douglas M. Cyr
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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17
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Allan KM, Farrow N, Donnelley M, Jaffe A, Waters SA. Treatment of Cystic Fibrosis: From Gene- to Cell-Based Therapies. Front Pharmacol 2021; 12:639475. [PMID: 33796025 PMCID: PMC8007963 DOI: 10.3389/fphar.2021.639475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
Prognosis of patients with cystic fibrosis (CF) varies extensively despite recent advances in targeted therapies that improve CF transmembrane conductance regulator (CFTR) function. Despite being a multi-organ disease, extensive lung tissue destruction remains the major cause of morbidity and mortality. Progress towards a curative treatment strategy that implements a CFTR gene addition-technology to the patients’ lungs has been slow and not yet developed beyond clinical trials. Improved delivery vectors are needed to overcome the body’s defense system and ensure an efficient and consistent clinical response before gene therapy is suitable for clinical care. Cell-based therapy–which relies on functional modification of allogenic or autologous cells ex vivo, prior to transplantation into the patient–is now a therapeutic reality for various diseases. For CF, pioneering research has demonstrated proof-of-principle for allogenic transplantation of cultured human airway stem cells into mouse airways. However, applying a cell-based therapy to the human airways has distinct challenges. We review CF gene therapies using viral and non-viral delivery strategies and discuss current advances towards autologous cell-based therapies. Progress towards identification, correction, and expansion of a suitable regenerative cell, as well as refinement of pre-cell transplant lung conditioning protocols is discussed.
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Affiliation(s)
- Katelin M Allan
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia
| | - Nigel Farrow
- Respiratory and Sleep Medicine, Women's and Children's Health Network, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Martin Donnelley
- Respiratory and Sleep Medicine, Women's and Children's Health Network, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, Australia
| | - Shafagh A Waters
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, Australia
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18
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Egan ME. Emerging technologies for cystic fibrosis transmembrane conductance regulator restoration in all people with CF. Pediatr Pulmonol 2021; 56 Suppl 1:S32-S39. [PMID: 32681713 PMCID: PMC8114183 DOI: 10.1002/ppul.24965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Abstract
Although effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has the potential to change the lives of many patients with cystic fibrosis (CF), it is unlikely that these drugs will be a game changing therapy for all. There are about 10% of patients with CF who don't produce a mutant protein tomodulate, potentiate, or optimize and for these patients such therapies are unlikely to be of significant benefit. There is a need to develop new therapeutic approaches that can work for this patient population and can advance CF therapies. These new therapies will be genetic-based therapies and each approach will result in functional CFTR protein inpreviously affected CF cells. In this review we will examine the potential of RNA therapies, gene transfer therapies, and gene editing therapies for the treatment of CF as well as the challenges that will need to be facedas we harness the power of these emerging therapies towards a one-time cure.
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Affiliation(s)
- Marie E Egan
- Division of Pulmonary Allergy Immunology Sleep Medicine, Department of Pediatrics, School of Medicine, Yale University, New Haven, Connecticut
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19
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Savant AP, McColley SA. Cystic fibrosis year in review 2019: Section 1 CFTR modulators. Pediatr Pulmonol 2020; 55:3236-3242. [PMID: 32833326 DOI: 10.1002/ppul.25039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
Abstract
During the year 2019, research and case reports/series in the field of cystic fibrosis (CF) were in abundance. To adequately address the large body of CF research published during 2019, the CF year in review will be divided into three sections. This report is the first section, focusing specifically on new research related to cystic fibrosis transmembrane conductance regulator modulator therapy. Additional sections will concentrate on pulmonary and infections research and the multisystem effects of CF. It is an exciting time to be providing care for patients and their families with CF with all the exciting new discoveries that will be shared in these reviews.
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Affiliation(s)
- Adrienne P Savant
- Children's Hospital of New Orleans, New Orleans, Louisiana.,Department of Pediatrics, Division of Pulmonary Medicine, Tulane University School of Medicine, New Orleans, Illinois
| | - Susanna A McColley
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Stanley Manne Children's Research Institute, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
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20
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Amaral MD. How to determine the mechanism of action of CFTR modulator compounds: A gateway to theranostics. Eur J Med Chem 2020; 210:112989. [PMID: 33190956 DOI: 10.1016/j.ejmech.2020.112989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The greatest challenge of 21st century biology is to fully understand mechanisms of disease to drive new approaches and medical innovation. Parallel to this is the huge biomedical endeavour of treating people through personalized medicine. Until now all CFTR modulator drugs that have entered clinical trials have been genotype-dependent. An emerging alternative is personalized/precision medicine in CF, i.e., to determine whether rare CFTR mutations respond to existing (or novel) CFTR modulator drugs by pre-assessing them directly on patient's tissues ex vivo, an approach also now termed theranostics. To administer the right drug to the right person it is essential to understand how drugs work, i.e., to know their mechanism of action (MoA), so as to predict their applicability, not just in certain mutations but also possibly in other diseases that share the same defect/defective pathway. Moreover, an understanding the MoA of a drug before it is tested in clinical trials is the logical path to drug discovery and can increase its chance for success and hence also approval. In conclusion, the most powerful approach to determine the MoA of a compound is to understand the underlying biology. Novel large datasets of intervenients in most biological processes, namely those emerging from the post-genomic era tools, are available and should be used to help in this task.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal.
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21
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Wang S, Lin L, Wang Y, Wang A, Liu Z, Wu S, Lan X, Jia J, Zhang Y, Yuan F, Wang C, Luo X, Sun X, Avula SK, Tolaymat A, Liu C, Ren Y, Chen Y. Novel homozygous mutation in the FBXL4 gene is associated with mitochondria DNA depletion syndrome-13. J Neurol Sci 2020; 416:116948. [PMID: 32559514 DOI: 10.1016/j.jns.2020.116948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Mitochondrial DNA depletion syndrome-13 (MTDPS13) is caused by mutations in FBXL4 (F-box and leucine-rich repeat protein 4), a nuclear gene encoding an F-box protein that plays a role in maintaining mtDNA integrity and stability. METHODS We identified a novel homozygous FBXL4 gene mutation, c.993dupA (p.L332Tfs*3), in a 1-year-old girl of Han Chinese descent. We performed three-dimensional protein structural analysis and targeted mtDNA next-generation sequencing. We analysed FBXL4 expression and mitochondrial DNA level, and reviewed mutations reported in FBXL4-related literature. RESULTS This mutation resulted in premature termination of translation and loss of 288 amino acids from C-terminus. A three-dimensional structural analysis revealed that conserved LRR domains were lost in mutant FBXL4 protein, which likely affected its ability to form protein-protein interactions. There were no differences in FBXL4 mRNA expression levels between the patient and her parents. There were no mtDNA mutations in either the patient or her parents. However, ND1/GAPDH ratio in lymphocytes and urine, which represents mtDNA/nuclear DNA ratio, showed that the number of mitochondrial genomes was significantly lower in the patient than in her parents or wild-type subjects. CONCLUSION Homozygous FBXL4 gene mutation, c.993dupA, can cause mitochondrial dysfunction, and LRR region is especially important for FBXL4 protein function.
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Affiliation(s)
- Simei Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China; Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, Peoria, IL 61637, USA
| | - Longlong Lin
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Yilin Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Anqi Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Zhao Liu
- Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, Peoria, IL 61637, USA
| | - Shengnan Wu
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Xiaoping Lan
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai 201202, China
| | - Yuanfeng Zhang
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Fang Yuan
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Chunmei Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Xiaona Luo
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Xiaomin Sun
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Sreenivas K Avula
- Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, Peoria, IL 61637, USA
| | - Abdullah Tolaymat
- Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, Peoria, IL 61637, USA
| | | | - Yun Ren
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China
| | - Yucai Chen
- Department of Neurology, Shanghai Children's Hospital, Shanghai JiaoTong University, Shanghai 200062, China.
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22
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Perego MGL, Galli N, Nizzardo M, Govoni A, Taiana M, Bresolin N, Comi GP, Corti S. Current understanding of and emerging treatment options for spinal muscular atrophy with respiratory distress type 1 (SMARD1). Cell Mol Life Sci 2020; 77:3351-3367. [PMID: 32123965 PMCID: PMC11104977 DOI: 10.1007/s00018-020-03492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
Spinal muscular atrophy (SMA) with respiratory distress type 1 (SMARD1) is an autosomal recessive motor neuron disease that is characterized by distal and proximal muscle weakness and diaphragmatic palsy that leads to respiratory distress. Without intervention, infants with the severe form of the disease die before 2 years of age. SMARD1 is caused by mutations in the IGHMBP2 gene that determine a deficiency in the encoded IGHMBP2 protein, which plays a critical role in motor neuron survival because of its functions in mRNA processing and maturation. Although it is rare, SMARD1 is the second most common motor neuron disease of infancy, and currently, treatment is primarily supportive. No effective therapy is available for this devastating disease, although multidisciplinary care has been an essential element of the improved quality of life and life span extension in these patients in recent years. The objectives of this review are to discuss the current understanding of SMARD1 through a summary of the presently known information regarding its clinical presentation and pathogenesis and to discuss emerging therapeutic approaches. Advances in clinical care management have significantly extended the lives of individuals affected by SMARD1 and research into the molecular mechanisms that lead to the disease has identified potential strategies for intervention that target the underlying causes of SMARD1. Gene therapy via gene replacement or gene correction provides the potential for transformative therapies to halt or possibly prevent neurodegenerative disease in SMARD1 patients. The recent approval of the first gene therapy approach for SMA associated with mutations in the SMN1 gene may be a turning point for the application of this strategy for SMARD1 and other genetic neurological diseases.
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Affiliation(s)
- Martina G L Perego
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Noemi Galli
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Monica Nizzardo
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Alessandra Govoni
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Michela Taiana
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Nereo Bresolin
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Giacomo P Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Stefania Corti
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy.
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
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23
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Adachi H, Yu YT. Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent. RNA (NEW YORK, N.Y.) 2020; 26:1247-1256. [PMID: 32434780 PMCID: PMC7430670 DOI: 10.1261/rna.076042.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 05/26/2023]
Abstract
We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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24
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Gianesello L, Ceol M, Bertoldi L, Terrin L, Priante G, Murer L, Peruzzi L, Giordano M, Paglialonga F, Cantaluppi V, Musetti C, Valle G, Del Prete D, Anglani F. Genetic Analyses in Dent Disease and Characterization of CLCN5 Mutations in Kidney Biopsies. Int J Mol Sci 2020; 21:ijms21020516. [PMID: 31947599 PMCID: PMC7014080 DOI: 10.3390/ijms21020516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 11/16/2022] Open
Abstract
Dent disease (DD), an X-linked renal tubulopathy, is mainly caused by loss-of-function mutations in CLCN5 (DD1) and OCRL genes. CLCN5 encodes the ClC-5 antiporter that in proximal tubules (PT) participates in the receptor-mediated endocytosis of low molecular weight proteins. Few studies have analyzed the PT expression of ClC-5 and of megalin and cubilin receptors in DD1 kidney biopsies. About 25% of DD cases lack mutations in either CLCN5 or OCRL genes (DD3), and no other disease genes have been discovered so far. Sanger sequencing was used for CLCN5 gene analysis in 158 unrelated males clinically suspected of having DD. The tubular expression of ClC-5, megalin, and cubilin was assessed by immunolabeling in 10 DD1 kidney biopsies. Whole exome sequencing (WES) was performed in eight DD3 patients. Twenty-three novel CLCN5 mutations were identified. ClC-5, megalin, and cubilin were significantly lower in DD1 than in control biopsies. The tubular expression of ClC-5 when detected was irrespective of the type of mutation. In four DD3 patients, WES revealed 12 potentially pathogenic variants in three novel genes (SLC17A1, SLC9A3, and PDZK1), and in three genes known to be associated with monogenic forms of renal proximal tubulopathies (SLC3A, LRP2, and CUBN). The supposed third Dent disease-causing gene was not discovered.
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Affiliation(s)
- Lisa Gianesello
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
| | - Monica Ceol
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
| | - Loris Bertoldi
- CRIBI Biotechnology Centre, University of Padua, 35131 Padua, Italy; (L.B.); (G.V.)
| | - Liliana Terrin
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
| | - Giovanna Priante
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
| | - Luisa Murer
- Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women’s and Children’s Health, Padua University Hospital, 35128 Padua, Italy;
| | - Licia Peruzzi
- Pediatric Nephrology Unit, Regina Margherita Children’s Hospital, 10126 CDSS Turin, Italy;
| | - Mario Giordano
- Pediatric Nephrology Unit, University Hospital, P.O. Giovanni XXIII, 70126 Bari, Italy;
| | - Fabio Paglialonga
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS, Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Vincenzo Cantaluppi
- Nephrology and Kidney Transplantation Unit, Department of Translational Medicine, University of Piemonte Orientale (UPO), 28100 Novara, Italy; (V.C.); (C.M.)
| | - Claudio Musetti
- Nephrology and Kidney Transplantation Unit, Department of Translational Medicine, University of Piemonte Orientale (UPO), 28100 Novara, Italy; (V.C.); (C.M.)
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, 35131 Padua, Italy; (L.B.); (G.V.)
| | - Dorella Del Prete
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
| | - Franca Anglani
- Laboratory of Histomorphology and Molecular Biology of the Kidney, Clinical Nephrology, Department of Medicine—DIMED, University of Padua, 35128 Padua, Italy; (L.G.); (M.C.); (L.T.); (G.P.); (D.D.P.)
- CRIBI Biotechnology Centre, University of Padua, 35131 Padua, Italy; (L.B.); (G.V.)
- Correspondence: ; Tel.: +39-049-8212-155
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Sarret C, Ashkavand Z, Paules E, Dorboz I, Pediaditakis P, Sumner S, Eymard-Pierre E, Francannet C, Krupenko NI, Boespflug-Tanguy O, Krupenko SA. Deleterious mutations in ALDH1L2 suggest a novel cause for neuro-ichthyotic syndrome. NPJ Genom Med 2019; 4:17. [PMID: 31341639 PMCID: PMC6650503 DOI: 10.1038/s41525-019-0092-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/03/2019] [Indexed: 01/06/2023] Open
Abstract
Neuro-ichthyotic syndromes are a group of rare genetic diseases mainly associated with perturbations in lipid metabolism, intracellular vesicle trafficking, or glycoprotein synthesis. Here, we report a patient with a neuro-ichthyotic syndrome associated with deleterious mutations in the ALDH1L2 (aldehyde dehydrogenase 1 family member L2) gene encoding for mitochondrial 10-formyltetrahydrofolate dehydrogenase. Using fibroblast culture established from the ALDH1L2-deficient patient, we demonstrated that the enzyme loss impaired mitochondrial function affecting both mitochondrial morphology and the pool of metabolites relevant to β-oxidation of fatty acids. Cells lacking the enzyme had distorted mitochondria, accumulated acylcarnitine derivatives and Krebs cycle intermediates, and had lower ATP and increased ADP/AMP indicative of a low energy index. Re-expression of functional ALDH1L2 enzyme in deficient cells restored the mitochondrial morphology and the metabolic profile of fibroblasts from healthy individuals. Our study underscores the role of ALDH1L2 in the maintenance of mitochondrial integrity and energy balance of the cell, and suggests the loss of the enzyme as the cause of neuro-cutaneous disease.
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Affiliation(s)
- Catherine Sarret
- IGCNC, Institut Pascal, UMR CNRS-UCA-SIGMA, Aubière, France.,2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Zahra Ashkavand
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA
| | - Evan Paules
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Imen Dorboz
- 5INSERM UMR1141, DHU PROTECT, PARIS-DIDEROT, University Sorbonne Paris-Cite, Paris, France
| | - Peter Pediaditakis
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA
| | - Susan Sumner
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Eléonore Eymard-Pierre
- 2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Christine Francannet
- 2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Natalia I Krupenko
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Odile Boespflug-Tanguy
- 5INSERM UMR1141, DHU PROTECT, PARIS-DIDEROT, University Sorbonne Paris-Cite, Paris, France.,6Department of Child Neurology and Metabolic Disorders, LEUKOFRANCE, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sergey A Krupenko
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
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26
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Clarke LA, Awatade NT, Felício VM, Silva IA, Calucho M, Pereira L, Azevedo P, Cavaco J, Barreto C, Bertuzzo C, Gartner S, Beekman J, Amaral MD. The effect of premature termination codon mutations on CFTR mRNA abundance in human nasal epithelium and intestinal organoids: a basis for read-through therapies in cystic fibrosis. Hum Mutat 2018; 40:326-334. [PMID: 30488522 DOI: 10.1002/humu.23692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/08/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
A major challenge in cystic fibrosis (CF) research is applying mutation-specific therapy to individual patients with diverse and rare CF transmembrane conductance regulator (CFTR) genotypes. Read-through agents are currently the most promising approach for Class I mutations that introduce premature termination codons (PTCs) into CFTR mRNA. However, variations in degradation of PTC containing transcripts by nonsense mediated decay (NMD) might lower read-through efficacy. Allele specific quantitative real time (qRT)-PCR was used to measure variations in CFTR mRNA abundance for several PTC mutations in respiratory cells and intestinal organoids. The majority of PTC mutations were associated with reduced levels of relative mRNA transcript abundance (∼33% and 26% of total CFTR mRNA in respiratory cells and intestinal organoids, respectively, compared to >50% for non-PTC causing mutations). These levels were generally not affected by PTC mutation type or position, but there could be twofold variations between individuals bearing the same genotype. Most PTC mutations in CFTR are subject to similar levels of NMD, which reduce but do not abolish PTC bearing mRNAs. Measurement of individual NMD levels in intestinal organoids and HNE cells might, therefore, be useful in predicting efficacy of PTC read-through in the context of personalized CFTR modulator therapy.
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Affiliation(s)
- Luka A Clarke
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Nikhil T Awatade
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Veronica M Felício
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Iris A Silva
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Maite Calucho
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Luisa Pereira
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Pilar Azevedo
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - José Cavaco
- Centro de Referência de Fibrose Quística, Hospital de Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisboa, Portugal
| | - Celeste Barreto
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Carmen Bertuzzo
- Human Genetics Department, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Silvia Gartner
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Jeffrey Beekman
- Department of Pediatric Pulmonology, UMCU, Utrecht, Netherlands
| | - Margarida D Amaral
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
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Forsythe E, Kenny J, Bacchelli C, Beales PL. Managing Bardet-Biedl Syndrome-Now and in the Future. Front Pediatr 2018; 6:23. [PMID: 29487844 PMCID: PMC5816783 DOI: 10.3389/fped.2018.00023] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Bardet-Biedl syndrome is a rare autosomal recessive multisystem disorder caused by defects in genes encoding for proteins that localize to the primary cilium/basal body complex. Twenty-one disease-causing genes have been identified to date. It is one of the most well-studied conditions in the family of diseases caused by defective cilia collectively known as ciliopathies. In this review, we provide an update on diagnostic developments, clinical features, and progress in the management of Bardet-Biedl syndrome. Advances in diagnostic technologies including exome and whole genome sequencing are expanding the spectrum of patients who are diagnosed with Bardet-Biedl syndrome and increasing the number of cases with diagnostic uncertainty. As a result of the diagnostic developments, a small number of patients with only one or two clinical features of Bardet-Biedl syndrome are being diagnosed. Our understanding of the syndrome-associated renal disease has evolved and is reviewed here. Novel interventions are developing at a rapid pace and are explored in this review including genetic therapeutics such as gene therapy, exon skipping therapy, nonsense suppression therapy, and gene editing. Other non-genetic therapies such as gene repurposing, targeted therapies, and non-pharmacological interventions are also discussed.
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Affiliation(s)
- Elizabeth Forsythe
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joanna Kenny
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Philip L Beales
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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