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Karachanak-Yankova S, Serbezov D, Antov G, Stancheva M, Mihaylova M, Hadjidekova S, Toncheva D, Pashov A, Belejanska D, Zhelev Y, Petrova M, Mehrabian S, Traykov L. Rare Pathogenic Variants in Pooled Whole-Exome Sequencing Data Suggest Hyperammonemia as a Possible Cause of Dementia Not Classified as Alzheimer's Disease or Frontotemporal Dementia. Genes (Basel) 2024; 15:753. [PMID: 38927689 PMCID: PMC11202446 DOI: 10.3390/genes15060753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The genetic bases of Alzheimer's disease (AD) and frontotemporal dementia (FTD) have been comprehensively studied, which is not the case for atypical cases not classified into these diagnoses. In the present study, we aim to contribute to the molecular understanding of the development of non-AD and non-FTD dementia due to hyperammonemia caused by mutations in urea cycle genes. The analysis was performed by pooled whole-exome sequencing (WES) of 90 patients and by searching for rare pathogenic variants in autosomal genes for enzymes or transporters of the urea cycle pathway. The survey returned two rare pathogenic coding mutations leading to citrullinemia type I: rs148918985, p.Arg265Cys, C>T; and rs121908641, p.Gly390Arg, G>A in the argininosuccinate synthase 1 (ASS1) gene. The p.Arg265Cys variant leads to enzyme deficiency, whereas p.Gly390Arg renders the enzyme inactive. These variants found in simple or compound heterozygosity can lead to the late-onset form of citrullinemia type I, associated with high ammonia levels, which can lead to cerebral dysfunction and thus to the development of dementia. The presence of urea cycle disorder-causing mutations can be used for the early initiation of antihyperammonemia therapy in order to prevent the neurotoxic effects.
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Affiliation(s)
- Sena Karachanak-Yankova
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, 1431 Sofia, Bulgaria; (D.S.); (M.M.); (S.H.); (D.T.)
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, 1164 Sofia, Bulgaria;
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, 1431 Sofia, Bulgaria; (D.S.); (M.M.); (S.H.); (D.T.)
| | - Georgi Antov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Mikaela Stancheva
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, 1164 Sofia, Bulgaria;
| | - Marta Mihaylova
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, 1431 Sofia, Bulgaria; (D.S.); (M.M.); (S.H.); (D.T.)
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, 1431 Sofia, Bulgaria; (D.S.); (M.M.); (S.H.); (D.T.)
| | - Draga Toncheva
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, 1431 Sofia, Bulgaria; (D.S.); (M.M.); (S.H.); (D.T.)
- Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Anastas Pashov
- Department of Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Diyana Belejanska
- Department of Neurology, University Hospital ‘Alexandrovska’, 1431 Sofia, Bulgaria; (D.B.); (Y.Z.); (M.P.); (S.M.); (L.T.)
| | - Yavor Zhelev
- Department of Neurology, University Hospital ‘Alexandrovska’, 1431 Sofia, Bulgaria; (D.B.); (Y.Z.); (M.P.); (S.M.); (L.T.)
| | - Mariya Petrova
- Department of Neurology, University Hospital ‘Alexandrovska’, 1431 Sofia, Bulgaria; (D.B.); (Y.Z.); (M.P.); (S.M.); (L.T.)
| | - Shima Mehrabian
- Department of Neurology, University Hospital ‘Alexandrovska’, 1431 Sofia, Bulgaria; (D.B.); (Y.Z.); (M.P.); (S.M.); (L.T.)
| | - Latchezar Traykov
- Department of Neurology, University Hospital ‘Alexandrovska’, 1431 Sofia, Bulgaria; (D.B.); (Y.Z.); (M.P.); (S.M.); (L.T.)
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Duff C, Baruteau J. Modelling urea cycle disorders using iPSCs. NPJ Regen Med 2022; 7:56. [PMID: 36163209 PMCID: PMC9513077 DOI: 10.1038/s41536-022-00252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
The urea cycle is a liver-based pathway enabling disposal of nitrogen waste. Urea cycle disorders (UCDs) are inherited metabolic diseases caused by deficiency of enzymes or transporters involved in the urea cycle and have a prevalence of 1:35,000 live births. Patients present recurrent acute hyperammonaemia, which causes high rate of death and neurological sequelae. Long-term therapy relies on a protein-restricted diet and ammonia scavenger drugs. Currently, liver transplantation is the only cure. Hence, high unmet needs require the identification of effective methods to model these diseases to generate innovative therapeutics. Advances in both induced pluripotent stem cells (iPSCs) and genome editing technologies have provided an invaluable opportunity to model patient-specific phenotypes in vitro by creating patients’ avatar models, to investigate the pathophysiology, uncover novel therapeutic targets and provide a platform for drug discovery. This review summarises the progress made thus far in generating 2- and 3-dimensional iPSCs models for UCDs, the challenges encountered and how iPSCs offer future avenues for innovation in developing the next-generation of therapies for UCDs.
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Affiliation(s)
- Claire Duff
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Julien Baruteau
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK. .,National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK. .,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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Xiong M, Chen M. Citrullinemia type I in Chinese children: Identification of two novel argininosuccinate synthetase gene mutations. Front Pediatr 2022; 10:992156. [PMID: 36263152 PMCID: PMC9574338 DOI: 10.3389/fped.2022.992156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND In this study, we evaluated the clinical characteristics, prognosis, and gene mutations of five children with citrullinemia type I (CTLN1) diagnosed in our department and identified two novel ASS1 gene mutations. METHODS We examined the clinical characteristics, prognosis, and gene mutations of the five children through data collection, tandem mass spectrometry, and whole-exon sequencing. MutationTaster, regSNP-intron, and SWISS-MODEL were used for bioinformatic analysis to evaluate the two novel gene mutations. We analyzed differences in blood ammonia and citrulline levels based on clinical phenotypes. Finally, we reviewed the medical literature describing Chinese children with CTLN1. RESULTS ASS1 C773 + 6T > G and c.848 delA as well as c.952_953 del insTT and c.133G > A have not been previously reported in the Human Gene Mutation Database. Using MutationTaster and regSNP-intron, we predicted that these mutations affected protein function. The 3D structure obtained using SWISS-MODEL supported this prediction. Through comparative analysis showed that the ammonia level of the neonatal type was markedly higher than that of other types, whereas citrulline levels did not differ between groups. CONCLUSION We identified two novel mutations that cause disease. The blood ammonia level of neonatal form citrullinemia was markedly higher than that of other types. The genotype-phenotype association in Chinese patients remains unclear and should be further evaluated in genetic studies of larger sample sizes.
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Affiliation(s)
- Mei Xiong
- Department of Pediatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Mingwu Chen
- Department of Pediatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Deng J, Li D, Mei H, Tang L, Wang HF, Hu Y. Novel deep intronic mutation in the coagulation factor XIII a chain gene leading to unexpected RNA splicing in a patient with factor XIII deficiency. BMC MEDICAL GENETICS 2020; 21:9. [PMID: 31914974 PMCID: PMC6950900 DOI: 10.1186/s12881-019-0944-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/24/2019] [Indexed: 11/24/2022]
Abstract
Background Coagulation factor XIII (FXIII) plays an essential role in maintaining hemostasis by crosslinking fibrin. Deficiency in FXIII affects clot stability and increases the risk of severe bleeding. Congenital FXIII deficiency is a rare disease. Recently, we identified a Chinese family with FXIII deficiency and investigated the pathogenesis of congenital FXIII deficiency, contributing non-coding pathogenic variants. Methods We performed common tests, coding sequencing by targeted next-generation sequencing (NGS), whole-genome sequencing and splice-sites prediction algorithms. The pathogenesis was investigated via minigene and nonsense-mediated mRNA decay (NMD) by experiments in vitro. Results The proband is homozygote for a novel deep intronic c.799-12G > A mutation in the F13A1 gene. Through direct sequencing of the minigenes mRNA, we found 10 bases of intron 6 insert in the mRNA of mutant minigenes mRNA. The relative expression of EGFP-F13A1 was higher by suppression of NMD in vitro. Furthermore, we found the proband with enhanced thrombin generation (TG). Conclusion We reported a novel deep intronic c.799-12G > A mutation of F13A1 which produced a new acceptor site and frame shifting during translation introducing a premature termination codon. Our results support the premature termination codon triggered NMD. We need to pay attention to the position of potential alterable splicing sites while counselling and genetic test. The finding of enhanced TG indicated that we should be aware of the risk of thrombosis in patients with FXIII deficiency during replacement therapy.
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Affiliation(s)
- Jun Deng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.,Hubei Clinical and Research Center of Thrombosis and Hemostasis, Wuhan, Hubei, People's Republic of China
| | - Dan Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.,Hubei Clinical and Research Center of Thrombosis and Hemostasis, Wuhan, Hubei, People's Republic of China
| | - Liang Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.,Hubei Clinical and Research Center of Thrombosis and Hemostasis, Wuhan, Hubei, People's Republic of China
| | - Hua-Fang Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.,Hubei Clinical and Research Center of Thrombosis and Hemostasis, Wuhan, Hubei, People's Republic of China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China. .,Hubei Clinical and Research Center of Thrombosis and Hemostasis, Wuhan, Hubei, People's Republic of China.
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Lin Y, Gao H, Lu B, Zhou S, Zheng T, Lin W, Zhu L, Jiang M, Fu Q. Citrullinemia type I is associated with a novel splicing variant, c.773 + 4A > C, in ASS1: a case report and literature review. BMC MEDICAL GENETICS 2019; 20:110. [PMID: 31208364 PMCID: PMC6580464 DOI: 10.1186/s12881-019-0836-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Citrullinemia type I (CTLN1) is a rare autosomal recessive disorder of the urea cycle caused by a deficiency in the argininosuccinate synthetase (ASS1) enzyme due to mutations in the ASS1 gene. Only a few Chinese patients with CTLN1 have been reported, and ASS1 gene mutations have been identified sporadically in China. CASE PRESENTATION A Chinese family with one member affected with mild CTLN1 was enrolled. Targeted exome sequencing was performed on the proband, and Sanger sequencing was used to validate the detected mutation. We also reviewed the genetic and clinical characteristics of CTLN1 in Chinese patients that have been published to date. Newborn screening showed remarkably increased concentrations of citrulline with elevated ratios of citrulline/arginine and citrulline/phenylalanine, and the patient presented with a speech delay at age three. The urinary organic acid profiles were normal. A novel homozygous splicing variant c.773 + 4A > C in the ASS1 gene was identified in the proband, and it was predicted to affect splicing by in silico analysis. To date, only nine Chinese patients with CTLN1 have been reported, with a total of 15 ASS1 mutations identified and no high frequency or hot spot mutations found; the mutation spectrum of Chinese patients with CTLN1 was heterogeneous. CONCLUSIONS We described a mild Chinese CTLN1 case with a novel homozygous splicing variant c.773 + 4A > C and reviewed previous genotypes and phenotypes in Chinese patients with CTLN1. Thus, our findings contribute to understanding the molecular genetic background and clinical phenotype of CTLN1 in this population.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Hongzhi Gao
- Department of Central Laboratory, 2nd Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - Bin Lu
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, 310007, Zhejiang Province, China
| | - Shuang Zhou
- Department of Central Laboratory, 2nd Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - Tianwen Zheng
- Department of Pediatrics, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Weihua Lin
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China
| | - Lin Zhu
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, 310007, Zhejiang Province, China
| | - Mengyi Jiang
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, 310007, Zhejiang Province, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center, Quanzhou Maternity and Children's Hospital, 700 Fengze Street, Quanzhou, 362000, Fujian Province, China.
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Liu G, Wang X, Qin M, Sun L, Zhu J. A novel splicing mutation of ectodysplasin A gene responsible for hypohidrotic ectodermal dysplasia. Oral Dis 2018; 24:1101-1106. [PMID: 29676859 DOI: 10.1111/odi.12874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is characterized by hypohidrosis, hypodontia, sparse hair, and characteristic facial features. This condition is caused by an ectodysplasin A (EDA) gene mutation. In this study, we examined two HED pedigrees and investigated the molecular genetics of the defect. Direct sequencing analysis revealed a previously unidentified mutation in the EDA splice donor site (c.526 + 1G>A). The function of the mutant EDA gene was predicted through online investigations and subsequently confirmed by splicing analysis in vitro. The mutation resulted in the production of a truncated EDA-A1 protein caused by complete omission of exon 3. This novel functional skipping-splicing EDA mutation was considered to be the cause of HED in the two pedigrees reported here. Our findings, combined with those reported elsewhere, provide an improved understanding of the pathogenic mechanism of HED as well as important information for a genetic diagnosis.
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Affiliation(s)
- G Liu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - X Wang
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - M Qin
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - L Sun
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - J Zhu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
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Kremer LS, Wortmann SB, Prokisch H. "Transcriptomics": molecular diagnosis of inborn errors of metabolism via RNA-sequencing. J Inherit Metab Dis 2018; 41:525-532. [PMID: 29372369 PMCID: PMC5959960 DOI: 10.1007/s10545-017-0133-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/05/2017] [Accepted: 12/28/2017] [Indexed: 02/02/2023]
Abstract
Exome wide sequencing techniques have revolutionized molecular diagnostics in patients with suspected inborn errors of metabolism or neuromuscular disorders. However, the diagnostic yield of 25-60% still leaves a large fraction of individuals without a diagnosis. This indicates a causative role for non-exonic regulatory variants not covered by whole exome sequencing. Here we review how systematic RNA-sequencing analysis (RNA-seq, "transcriptomics") lead to a molecular diagnosis in 10-35% of patients in whom whole exome sequencing failed to do so. Importantly, RNA-sequencing based discoveries cannot only guide molecular diagnosis but might also unravel therapeutic intervention points such as antisense oligonucleotide treatment for splicing defects as recently reported for spinal muscular atrophy.
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Affiliation(s)
- Laura S Kremer
- Institute of Human Genetics, Technische Universität München, Trogerstrasse 32, 81675, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Saskia B Wortmann
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
- Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Trogerstrasse 32, 81675, Munich, Germany.
- Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany.
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Diez-Fernandez C, Rüfenacht V, Häberle J. Mutations in the Human Argininosuccinate Synthetase (ASS1) Gene, Impact on Patients, Common Changes, and Structural Considerations. Hum Mutat 2017; 38:471-484. [DOI: 10.1002/humu.23184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Diez-Fernandez
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
| | - Johannes Häberle
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
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Diez-Fernandez C, Wellauer O, Gemperle C, Rüfenacht V, Fingerhut R, Häberle J. Kinetic mutations in argininosuccinate synthetase deficiency: characterisation and in vitro correction by substrate supplementation. J Med Genet 2016; 53:710-9. [PMID: 27287393 DOI: 10.1136/jmedgenet-2016-103937] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/19/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Citrullinemia type 1 is an autosomal-recessive urea cycle disorder caused by mutations in the ASS1 gene and characterised by increased plasma citrulline concentrations. Of the ∼90 argininosuccinate synthetase (ASS) missense mutations reported, 21 map near the substrate (aspartate or citrulline) binding site, and thus are potential kinetic mutations whose decreased activities could be amenable to substrate supplementation. This article aims at characterising these 21 ASS mutations to prove their disease-causing role and to test substrate supplementation as a novel therapeutic approach. METHODS We used an Escherichia coli expression system to study all potentially kinetic ASS mutations. All mutant enzymes were nickel-affinity purified, their activity and kinetic parameters were measured using tandem mass spectrometry and their thermal stability using differential scanning fluorimetry. Structural rationalisation of the effects of these mutations was performed. RESULTS Of the characterised mutants, 13 were totally inactive while 8 exhibited decreased affinity for aspartate and citrulline. The activity of these eight kinetic mutations could be rescued to ∼10-99% of the wild-type using high l-aspartate concentrations. CONCLUSIONS Substrate supplementation raised in vitro the activity of eight citrullinemia type 1 mutations with reduced affinity for aspartate. As a direct translation of these results to the clinics, we propose to further evaluate the use of oxaloacetate, a nitrogen-free aspartate precursor and already available medical food (anti-ageing and brain stimulating, not considered as a drug by the US Food and Drug Administration), in patients with citrullinemia type 1 with decreased aspartate affinity. Although only patients with kinetic mutations would benefit, oxaloacetate could offer a safe novel treatment.
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Affiliation(s)
- Carmen Diez-Fernandez
- Division of Metabolism, University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - Olivia Wellauer
- Division of Metabolism, University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - Corinne Gemperle
- Division of Metabolism, University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism, University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - Ralph Fingerhut
- Neonatal Screening Laboratory, University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism, University Children's Hospital and Children's Research Center, Zurich, Switzerland
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