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Koshimizu E, Kato M, Misawa K, Uchiyama Y, Tsuchida N, Hamanaka K, Fujita A, Mizuguchi T, Miyatake S, Matsumoto N. Detection of hidden intronic DDC variant in aromatic L-amino acid decarboxylase deficiency by adaptive sampling. J Hum Genet 2024; 69:153-157. [PMID: 38216729 DOI: 10.1038/s10038-023-01217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Aromatic l-amino acid decarboxylase (AADC) deficiency is an autosomal recessive neurotransmitter disorder caused by pathogenic DOPA decarboxylase (DDC) variants. We previously reported Japanese siblings with AADC deficiency, which was confirmed by the lack of enzyme activity; however, only a heterozygous missense variant was detected. We therefore performed targeted long-read sequencing by adaptive sampling to identify any missing variants. Haplotype phasing and variant calling identified a novel deep intronic variant (c.714+255 C > A), which was predicted to potentially activate the noncanonical splicing acceptor site. Minigene assay revealed that wild-type and c.714+255 C > A alleles had different impacts on splicing. Three transcripts, including the canonical transcript, were detected from the wild-type allele, but only the noncanonical cryptic exon was produced from the variant allele, indicating that c.714+255 C > A was pathogenic. Target long-read sequencing may be used to detect hidden pathogenic variants in unresolved autosomal recessive cases with only one disclosed hit variant.
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Affiliation(s)
- Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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Chen S, Heendeniya SN, Le BT, Rahimizadeh K, Rabiee N, Zahra QUA, Veedu RN. Splice-Modulating Antisense Oligonucleotides as Therapeutics for Inherited Metabolic Diseases. BioDrugs 2024; 38:177-203. [PMID: 38252341 PMCID: PMC10912209 DOI: 10.1007/s40259-024-00644-7] [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] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The last decade (2013-2023) has seen unprecedented successes in the clinical translation of therapeutic antisense oligonucleotides (ASOs). Eight such molecules have been granted marketing approval by the United States Food and Drug Administration (US FDA) during the decade, after the first ASO drug, fomivirsen, was approved much earlier, in 1998. Splice-modulating ASOs have also been developed for the therapy of inborn errors of metabolism (IEMs), due to their ability to redirect aberrant splicing caused by mutations, thus recovering the expression of normal transcripts, and correcting the deficiency of functional proteins. The feasibility of treating IEM patients with splice-switching ASOs has been supported by FDA permission (2018) of the first "N-of-1" study of milasen, an investigational ASO drug for Batten disease. Although for IEM, owing to the rarity of individual disease and/or pathogenic mutation, only a low number of patients may be treated by ASOs that specifically suppress the aberrant splicing pattern of mutant precursor mRNA (pre-mRNA), splice-switching ASOs represent superior individualized molecular therapeutics for IEM. In this work, we first summarize the ASO technology with respect to its mechanisms of action, chemical modifications of nucleotides, and rational design of modified oligonucleotides; following that, we precisely provide a review of the current understanding of developing splice-modulating ASO-based therapeutics for IEM. In the concluding section, we suggest potential ways to improve and/or optimize the development of ASOs targeting IEM.
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Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Saumya Nishanga Heendeniya
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia.
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia.
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Chu WS, Ng J, Waddington SN, Kurian MA. Gene therapy for neurotransmitter-related disorders. J Inherit Metab Dis 2024; 47:176-191. [PMID: 38221762 PMCID: PMC11108624 DOI: 10.1002/jimd.12697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
Inborn errors of neurotransmitter (NT) metabolism are a group of rare, heterogenous diseases with predominant neurological features, such as movement disorders, autonomic dysfunction, and developmental delay. Clinical overlap with other disorders has led to delayed diagnosis and treatment, and some conditions are refractory to oral pharmacotherapies. Gene therapies have been developed and translated to clinics for paediatric inborn errors of metabolism, with 38 interventional clinical trials ongoing to date. Furthermore, efforts in restoring dopamine synthesis and neurotransmission through viral gene therapy have been developed for Parkinson's disease. Along with the recent European Medicines Agency (EMA) and Medicines and Healthcare Products Regulatory Agency (MHRA) approval of an AAV2 gene supplementation therapy for AADC deficiency, promising efficacy and safety profiles can be achieved in this group of diseases. In this review, we present preclinical and clinical advances to address NT-related diseases, and summarise potential challenges that require careful considerations for NT gene therapy studies.
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Affiliation(s)
- Wing Sum Chu
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Joanne Ng
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Simon N. Waddington
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Manju A. Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of NeurologyGreat Ormond Street Hospital for ChildrenLondonUK
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Himmelreich N, Montioli R, Bertoldi M, Carducci C, Leuzzi V, Gemperle C, Berner T, Hyland K, Thöny B, Hoffmann GF, Voltattorni CB, Blau N. Aromatic amino acid decarboxylase deficiency: Molecular and metabolic basis and therapeutic outlook. Mol Genet Metab 2019; 127:12-22. [PMID: 30952622 DOI: 10.1016/j.ymgme.2019.03.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 12/24/2022]
Abstract
Aromatic-l-amino acid decarboxylase (AADC) deficiency is an ultra-rare inherited autosomal recessive disorder characterized by sharply reduced synthesis of dopamine as well as other neurotransmitters. Symptoms, including hypotonia and movement disorders (especially oculogyric crisis and dystonia) as well as autonomic dysfunction and behavioral disorders, vary extensively and typically emerge in the first months of life. However, diagnosis is difficult, requiring analysis of metabolites in cerebrospinal fluid, assessment of plasma AADC activity, and/or DNA sequence analysis, and is frequently delayed for years. New metabolomics techniques promise early diagnosis of AADC deficiency by detection of 3-O-methyl-dopa in serum or dried blood spots. A total of 82 dopa decarboxylase (DDC) variants in the DDC gene leading to AADC deficiency have been identified and catalogued for all known patients (n = 123). Biochemical and bioinformatics studies provided insight into the impact of many variants. c.714+4A>T, p.S250F, p.R347Q, and p.G102S are the most frequent variants (cumulative allele frequency = 57%), and c.[714+4A>T];[714+4A>T], p.[S250F];[S250F], and p.[G102S];[G102S] are the most frequent genotypes (cumulative genotype frequency = 40%). Known or predicted molecular effect was defined for 79 variants. Most patients experience an unrelenting disease course with poor or no response to conventional medical treatments, including dopamine agonists, monoamine oxidase inhibitors, and pyridoxine derivatives. The advent of gene therapy represents a potentially promising new avenue for treatment of patients with AADC deficiency. Clinical studies based on the direct infusion of engineered adeno-associated virus type 2 vectors into the putamen have demonstrated acceptable safety and tolerability and encouraging improvement in motor milestones and cognitive symptoms. The success of gene therapy in AADC deficiency treatment will depend on timely diagnosis to facilitate treatment administration before the onset of neurologic damage.
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Affiliation(s)
- Nastassja Himmelreich
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Riccardo Montioli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Mariarita Bertoldi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Carla Carducci
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Corinne Gemperle
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | - Todd Berner
- Global Medical Affairs, PTC Therapeutics, South Plainfield, NJ, USA
| | - Keith Hyland
- Medical Neurogenetics Laboratories, Atlanta, GA, USA
| | - Beat Thöny
- Department of Pediatrics, Divisions of Metabolism and of Clinical Chemistry and Biochemistry, University of Zürich, Zürich, Switzerland
| | - Georg F Hoffmann
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany
| | - Carla B Voltattorni
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
| | - Nenad Blau
- Dietmar-Hopp Metabolic Center and Centre for Pediatrics and Adolescent Medicine, University Children's Hospital, Heidelberg, Germany.
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5
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Lee NC, Chien YH, Hwu WL. A review of aromatic l
-amino acid decarboxylase (AADC) deficiency in Taiwan. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:226-229. [DOI: 10.1002/ajmg.c.31670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Ni-Chung Lee
- Department of Medical Genetics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
- Department of Pediatrics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
- Department of Pediatrics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
- Department of Pediatrics; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
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