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Shen Z, Ma Y, Gao M, Gu L. Temporal metabolomics analysis reveals the metabolic patterns in goat cumulus cells during oocyte maturation. Gene 2024; 928:148772. [PMID: 39025339 DOI: 10.1016/j.gene.2024.148772] [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: 03/25/2024] [Revised: 06/30/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Cumulus cells play a crucial role in the oocyte growth and maturation processes through providing necessary nutrients and growth signals by gap junction communication. However, a global overview of metabolic events in goat cumulus cells is still lacking. In the present study, we collected cumulus cells from goat cumulus-oocyte complexes (COCs) at different developmental stages. Metabolomics analysis was performed to investigate the global metabolic patterns in cumulus cells during oocyte in vitro maturation. In particular, we revealed the several significantly altered metabolic pathways and metaboliccharacteristics in goat cumulus cells, including the accumulation of fatty acids, steroid hormones metabolism, active catabolism of arginine during meiotic resumption, and a progressive decline in nucleotide metabolism. In conclusion, the dataset generated by our metabolomic profiling will provide valuable information to understand the key metabolic pathways and metabolites involved in COCs development.
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Affiliation(s)
- Zhiyuan Shen
- College of Computer and Information Engineering, Tianjin Agricultural University, Tianjin 300392, China
| | - Yixin Ma
- College of Animal Science & Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ming Gao
- College of Animal Science & Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ling Gu
- College of Animal Science & Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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2
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Korasick DA, Buckley DP, Palpacelli A, Cursio I, Cesaroni E, Cheng J, Tanner JJ. Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1. Chem Biol Interact 2024; 394:110993. [PMID: 38604394 PMCID: PMC11073572 DOI: 10.1016/j.cbi.2024.110993] [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: 02/27/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Aldehyde dehydrogenase 7A1 (ALDH7A1) catalyzes a step of lysine catabolism. Certain missense mutations in the ALDH7A1 gene cause pyridoxine dependent epilepsy (PDE), a rare autosomal neurometabolic disorder with recessive inheritance that affects almost 1:65,000 live births and is classically characterized by recurrent seizures from the neonatal period. We report a biochemical, structural, and computational study of two novel ALDH7A1 missense mutations that were identified in a child with rare recurrent seizures from the third month of life. The mutations affect two residues in the oligomer interfaces of ALDH7A1, Arg134 and Arg441 (Arg162 and Arg469 in the HGVS nomenclature). The corresponding enzyme variants R134S and R441C (p.Arg162Ser and p.Arg469Cys in the HGVS nomenclature) were expressed in Escherichia coli and purified. R134S and R441C have 10,000- and 50-fold lower catalytic efficiency than wild-type ALDH7A1, respectively. Sedimentation velocity analytical ultracentrifugation shows that R134S is defective in tetramerization, remaining locked in a dimeric state even in the presence of the tetramer-inducing coenzyme NAD+. Because the tetramer is the active form of ALDH7A1, the defect in oligomerization explains the very low catalytic activity of R134S. In contrast, R441C exhibits wild-type oligomerization behavior, and the 2.0 Å resolution crystal structure of R441C complexed with NAD+ revealed no obvious structural perturbations when compared to the wild-type enzyme structure. Molecular dynamics simulations suggest that the mutation of Arg441 to Cys may increase intersubunit ion pairs and alter the dynamics of the active site gate. Our biochemical, structural, and computational data on two novel clinical variants of ALDH7A1 add to the complexity of the molecular determinants underlying pyridoxine dependent epilepsy.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - David P Buckley
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | | | - Ida Cursio
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Elisabetta Cesaroni
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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3
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Cong M, Li Z, Che Y, Li Y, Tian W, Lv J, Sun X. Metabolomics revealed more deleterious toxicity induced by the combined exposure of ammonia and nitrite on Ruditapes philippinarum compared to single exposure. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106398. [PMID: 38377938 DOI: 10.1016/j.marenvres.2024.106398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/26/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
NH3-N and NO2-N always co-exist in the aquatic environment, but there is not a clear opinion on their joint toxicities to the molluscs. Presently, clams Ruditapes philippinarum were challenged by environmental concentrations of NH3-N and NO2-N, singly or in combination, and analyzed by metabolomics approaches, enzyme assays and transmission electron microscope (TEM) observation. Results showed that some same KEGG pathways with different enriched-metabolites were detected in the three exposed groups within one day, and completely different profiles of metabolites were found in the rest of the exposure period. The combined exposure induced heavier and more lasting toxicities to the clams compared with their single exposure. ACP activity and the number of secondary lysosomes were significantly increased after the combined exposure. The present study shed light on the joint-toxicity mechanism of NH3-N and NO2-N, and provided fundamental data for the toxicity research on inorganic nitrogen.
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Affiliation(s)
- Ming Cong
- Ocean School, Yantai University, Yantai, 264005, China.
| | - Zhaoshun Li
- Ocean School, Yantai University, Yantai, 264005, China
| | - Yu Che
- Ocean School, Yantai University, Yantai, 264005, China
| | - Yuanmei Li
- Ocean School, Yantai University, Yantai, 264005, China
| | - Wenwen Tian
- Ocean School, Yantai University, Yantai, 264005, China
| | - Jiasen Lv
- Biology School, Yantai University, Yantai, 264005, China.
| | - Xiyan Sun
- Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
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Vikram PRH, Beeraka NM, Patel HB, Kumar P. RP-HPLC-DAD method development and validation of L-lysine hydrochloride: application to bulk drug substance and multivitamin oral suspension. ACCREDITATION AND QUALITY ASSURANCE 2023. [DOI: 10.1007/s00769-023-01544-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/13/2023] [Indexed: 09/25/2023]
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5
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Qi B, Zhang Y, Xu B, Zhang Y, Fei G, Lin L, Li Q. Metabolomic Characterization of Acute Ischemic Stroke Facilitates Metabolomic Biomarker Discovery. Appl Biochem Biotechnol 2022; 194:5443-5455. [DOI: 10.1007/s12010-022-04024-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
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6
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Leandro J, Houten SM. The lysine degradation pathway: Subcellular compartmentalization and enzyme deficiencies. Mol Genet Metab 2020; 131:14-22. [PMID: 32768327 DOI: 10.1016/j.ymgme.2020.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 02/07/2023]
Abstract
Lysine degradation via formation of saccharopine is a pathway confined to the mitochondria. The second pathway for lysine degradation, the pipecolic acid pathway, is not yet fully elucidated and known enzymes are localized in the mitochondria, cytosol and peroxisome. The tissue-specific roles of these two pathways are still under investigation. The lysine degradation pathway is clinically relevant due to the occurrence of two severe neurometabolic disorders, pyridoxine-dependent epilepsy (PDE) and glutaric aciduria type 1 (GA1). The existence of three other disorders affecting lysine degradation without apparent clinical consequences opens up the possibility to find alternative therapeutic strategies for PDE and GA1 through pathway modulation. A better understanding of the mechanisms, compartmentalization and interplay between the different enzymes and metabolites involved in lysine degradation is of utmost importance.
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Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Chen L, Chang R, Pan S, Xu J, Cao Q, Su G, Zhou C, Kijlstra A, Yang P. Plasma metabolomics study of Vogt-Koyanagi-Harada disease identifies potential diagnostic biomarkers. Exp Eye Res 2020; 196:108070. [PMID: 32439397 DOI: 10.1016/j.exer.2020.108070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/23/2022]
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a common type of uveitis in China, but the diagnosis criteria of VKH disease is controversial. The aim of this study was to investigate potential diagnostic plasma biomarkers for VKH disease. A case-control study including 55 VKH patients (28 active patients and 27 inactive VKH patients) and 30 healthy controls in a tertiary referral center was performed. The metabolic phenotype of VKH patients showed a significant difference compared to healthy controls. Fifteen differentially expressed metabolites (DEMs) were identified between active VKH patients and healthy controls and nine DEMs were found between inactive VKH patients and healthy controls after controlling variable importance in the projection (VIP) value > 1 and false discovery rate (FDR) < 0.05. D-mannose, stearic acid and L-lysine were shown to be potential diagnostic biomarkers which can discriminate active VKH patients from healthy controls with a diagnostic performance with AUC = 0.965, 0.936 and 0.910 respectively in independent diagnosis and an AUC = 0.999 when combined. Sarcosine was recognized as an independent potential biomarker which could distinguish inactive VKH patients from healthy controls. This study reveals a significant difference of plasma metabolic phenotype and identifies diagnostic biomarkers for VKH disease. Changes in the metabolic profile may provide clues towards the pathophysiology of VKH disease.
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Affiliation(s)
- Lin Chen
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Rui Chang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Su Pan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Jing Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Chunjiang Zhou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht, the Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China.
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Artiukhov AV, Grabarska A, Gumbarewicz E, Aleshin VA, Kähne T, Obata T, Kazantsev AV, Lukashev NV, Stepulak A, Fernie AR, Bunik VI. Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. Sci Rep 2020; 10:1886. [PMID: 32024885 PMCID: PMC7002488 DOI: 10.1038/s41598-020-58701-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
The biological significance of the DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) remains obscure due to its catalytic redundancy with the ubiquitous OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH). In this work, metabolic contributions of OADH and OGDH are discriminated by exposure of cells/tissues with different DHTKD1 expression to the synthesized phosphonate analogues of homologous 2-oxodicarboxylates. The saccharopine pathway intermediates and phosphorylated sugars are abundant when cellular expressions of DHTKD1 and OGDH are comparable, while nicotinate and non-phosphorylated sugars are when DHTKD1 expression is order(s) of magnitude lower than that of OGDH. Using succinyl, glutaryl and adipoyl phosphonates on the enzyme preparations from tissues with varied DHTKD1 expression reveals the contributions of OADH and OGDH to oxidation of 2-oxoadipate and 2-oxoglutarate in vitro. In the phosphonates-treated cells with the high and low DHTKD1 expression, adipate or glutarate, correspondingly, are the most affected metabolites. The marker of fatty acid β-oxidation, adipate, is mostly decreased by the shorter, OGDH-preferring, phosphonate, in agreement with the known OGDH dependence of β-oxidation. The longest, OADH-preferring, phosphonate mostly affects the glutarate level. Coupled decreases in sugars and nicotinate upon the OADH inhibition link the perturbation in glucose homeostasis, known in OADH mutants, to the nicotinate-dependent NAD metabolism.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aneta Grabarska
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Ewelina Gumbarewicz
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Vasily A Aleshin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Biochemistry, George W. Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, USA
| | | | | | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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Boonchaisri S, Stevenson T, Dias DA. Utilization of GC-MS untargeted metabolomics to assess the delayed response of glufosinate treatment of transgenic herbicide resistant (HR) buffalo grasses (Stenotaphrum secundatum L.). Metabolomics 2020; 16:22. [PMID: 31989303 DOI: 10.1007/s11306-020-1644-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Herbicide resistant (HR) buffalo grasses were genetically engineered to resist the non-selective herbicide, glufosinate in order to facilitate a modern, 'weeding program' which is highly effective in terms of minimizing costs and labor. The resistant trait was conferred by an insertion of the pat gene to allow for the production of the enzyme phosphinothricin acetyltransferase (PAT) to detoxify the glufosinate inhibitive effect. To date, there are only a few reports using metabolomics as well as molecular characterizations published for glufosinate-resistant crops with no reports on HR turfgrass. Therefore, for the first time, this study examines the metabolome of glufosinate-resistant buffalo grasses which not only will be useful to future growers but also the scientific community. OBJECTIVE A major aim of this present work is to characterize and evaluate the metabolic alterations which may arise from a genetic transformation of HR buffalo grasses by comprehensively using gas chromatography-mass spectrometry (GC-MS) based untargeted metabolomics. METHODS Eight-week old plants of 4 HR buffalo grasses, (93-1A, 93-2B, 93-3C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were selected for physiological, molecular and metabolomics experiments. Plants were either sprayed with 1, 5, 10 and 15% v/v of glufosinate to evaluate the visual injuries or submerged in 5% v/v of glufosinate 3 days prior to a GC-MS based untargeted metabolomics analysis. In contrast, the control group was treated with distilled water. Leaves were extracted in 1:1 methanol:water and then analysed, using an in-house GC-MS untargeted workflow. RESULTS Results identified 199 metabolites with only 6 of them (cis-aconitic acid, allantoin, cellobiose, glyceric acid, maltose and octadecanoic acid) found to be statistically significant (p < 0.05) between the HR and wild type buffalo grass varieties compared to the control experiment. Among these metabolites, unusual accumulation of allantoin was prominent and was an unanticipated effect of the pat gene insertion. As expected, glufosinate treatment caused significant metabolic alterations in the sensitive wild type, with the up-regulation of several amino acids (e.g. phenylalanine and isoleucine) which was likely due to glufosinate-induced senescence. The aminoacyl-tRNA biosynthetic pathway was identified as the most significant enriched pathway as a result of glufosinate effects because a number of its intermediates were amino acids. CONCLUSION HR buffalo grasses were very similar to its wild type comparator based on a comprehensive GC-MS based untargeted metabolomics and therefore, should guarantee the safe use of these HR buffalo grasses. The current metabolomics analyses not only confirmed the effects of glufosinate to up-regulate free amino acid pools in the sensitive wild type but also several alterations in sugar, sugar phosphate and organic acid metabolism have been reported.
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Affiliation(s)
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
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Biomarker profiling of vitamin responsive seizures: a potential tool to detect pediatric seizures of unknown aetiology. Bioanalysis 2019; 12:111-124. [PMID: 31854203 DOI: 10.4155/bio-2019-0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: Certain rare inborn errors of metabolism clinically present with intractable seizures that readily respond to vitamin therapy. If identified early, brain damage due to seizures can be prevented. Methodology: A LC-MS method was developed and validated for the simultaneous quantification of the biomarkers in selected vitamin responsive pediatric seizures from dried blood spots. Results: Application of the validated method to a seizure cohort of 46 patients indicated strong agreement of the method for clinical validity. Reference intervals for these biomarkers in dried blood spots were also determined for the population, after screening 956 neonates. Conclusion: The developed method was seen to be sensitive, linear, accurate and precise for testing vitamin responsive pediatric seizures.
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Simultaneous quantification of alpha-aminoadipic semialdehyde, piperideine-6-carboxylate, pipecolic acid and alpha-aminoadipic acid in pyridoxine-dependent epilepsy. Sci Rep 2019; 9:11371. [PMID: 31388081 PMCID: PMC6684619 DOI: 10.1038/s41598-019-47882-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/02/2019] [Indexed: 11/27/2022] Open
Abstract
The measurements of lysine metabolites provide valuable information for the rapid diagnosis of pyridoxine-dependent epilepsy (PDE). Here, we aimed to develop a sensitive method to simultaneously quantify multiple lysine metabolites in PDE, including α-aminoadipic semialdehyde (a-AASA), piperideine-6-carboxylate (P6C), pipecolic acid (PA) and α-aminoadipic acid (α-AAA) in plasma, serum, dried blood spots (DBS), urine and dried urine spots (DUS). Fifteen patients with molecularly confirmed PDE were detected using liquid chromatography-mass spectrometry (LC-MS/MS) method. Compared to the control groups, the concentrations of a-AASA, P6C and the sum of a-AASA and P6C (AASA-P6C) in all types of samples from PDE patients were markedly elevated. The PA and a-AAA concentrations ranges overlapped partially between PDE patients and control groups. The concentrations of all the analytes in plasma and serum, as well as in urine and DUS were highly correlated. Our study provided more options for the diverse sample collection in the biochemical tests according to practical requirements. With treatment modality of newly triple therapy investigated, biomarker study might play important role not only on diagnosis but also on treatment monitoring and fine tuning the diet. The persistently elevated analytes with good correlation between plasma and DBS, as well as urine and DUS made neonatal screening using DBS and DUS possible.
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Crowther LM, Mathis D, Poms M, Plecko B. New insights into human lysine degradation pathways with relevance to pyridoxine-dependent epilepsy due to antiquitin deficiency. J Inherit Metab Dis 2019; 42:620-628. [PMID: 30767241 DOI: 10.1002/jimd.12076] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/12/2019] [Indexed: 01/19/2023]
Abstract
Deficiency of antiquitin (ATQ), an enzyme involved in lysine degradation, is the major cause of vitamin B6 -dependent epilepsy. Accumulation of the potentially neurotoxic α-aminoadipic semialdehyde (AASA) may contribute to frequently associated developmental delay. AASA is formed by α-aminoadipic semialdehyde synthase (AASS) via the saccharopine pathway of lysine degradation, or, as has been postulated, by the pipecolic acid (PA) pathway, and then converted to α-aminoadipic acid by ATQ. The PA pathway has been considered to be the predominant pathway of lysine degradation in mammalian brain; however, this was refuted by recent studies in mouse. Consequently, inhibition of AASS was proposed as a potential new treatment option for ATQ deficiency. It is therefore of utmost importance to determine whether the saccharopine pathway is also predominant in human brain cells. The route of lysine degradation was analyzed by isotopic tracing studies in cultured human astrocytes, ReNcell CX human neuronal progenitor cells and human fibroblasts, and expression of enzymes of the two lysine degradation pathways was determined by Western blot. Lysine degradation was only detected through the saccharopine pathway in all cell types studied. The enrichment of 15 N-glutamate as a side product of AASA formation through AASS furthermore demonstrated activity of the saccharopine pathway. We provide first evidence that the saccharopine pathway is the major route of lysine degradation in cultured human brain cells. These results support inhibition of the saccharopine pathway as a new treatment option for ATQ deficiency.
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Affiliation(s)
- Lisa M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - Déborah Mathis
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
- Department of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Zurich, Switzerland
| | - Martin Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
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13
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Wempe MF, Kumar A, Kumar V, Choi YJ, Swanson MA, Friederich MW, Hyland K, Yue WW, Van Hove JLK, Coughlin CR. Identification of a novel biomarker for pyridoxine-dependent epilepsy: Implications for newborn screening. J Inherit Metab Dis 2019; 42:565-574. [PMID: 30663059 DOI: 10.1002/jimd.12059] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 01/11/2019] [Indexed: 11/12/2022]
Abstract
Pyridoxine-dependent epilepsy (PDE) is often characterized as an early onset epileptic encephalopathy with dramatic clinical improvement following pyridoxine supplementation. Unfortunately, not all patients present with classic neonatal seizures or respond to an initial pyridoxine trial, which can result in the under diagnosis of this treatable disorder. Restriction of lysine intake and transport is associated with improved neurologic outcomes, although treatment should be started in the first year of life to be effective. Because of the documented diagnostic delay and benefit of early treatment, we aimed to develop a newborn screening method for PDE. Previous studies have demonstrated the accumulation of Δ1 -piperideine-6-carboxylate and α-aminoadipic semialdehyde in individuals with PDE, although these metabolites are unstable at room temperature (RT) limiting their utility for newborn screening. As a result, we sought to identify a biomarker that could be applied to current newborn screening paradigms. We identified a novel metabolite, 6-oxo-pipecolate (6-oxo-PIP), which accumulates in substantial amounts in blood, plasma, urine, and cerebral spinal fluid of individuals with PDE. Using a stable isotope-labeled internal standard, we developed a nonderivatized liquid chromatography tandem mass spectrometry-based method to quantify 6-oxo-PIP. This method replicates the analytical techniques used in many laboratories and could be used with few modifications in newborn screening programs. Furthermore, 6-oxo-PIP was measurable in urine for 4 months even when stored at RT. Herein, we report a novel biomarker for PDE that is stable at RT and can be quantified using current newborn screening techniques.
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Affiliation(s)
- Michael F Wempe
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Amit Kumar
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Vijay Kumar
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Yu J Choi
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Michael A Swanson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado
| | - Keith Hyland
- Medical Neurogenetics Laboratories, LLC, Atlanta, Georgia
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado
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14
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Leandro J, Violante S, Argmann CA, Hagen J, Dodatko T, Bender A, Zhang W, Williams EG, Bachmann AM, Auwerx J, Yu C, Houten SM. Mild inborn errors of metabolism in commonly used inbred mouse strains. Mol Genet Metab 2019; 126:388-396. [PMID: 30709776 PMCID: PMC6535113 DOI: 10.1016/j.ymgme.2019.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Inbred mouse strains are a cornerstone of translational research but paradoxically many strains carry mild inborn errors of metabolism. For example, α-aminoadipic acidemia and branched-chain ketoacid dehydrogenase deficiency are known in C57BL/6J mice. Using RNA sequencing, we now reveal the causal variants in Dhtkd1 and Bckdhb, and the molecular mechanism underlying these metabolic defects. C57BL/6J mice have decreased Dhtkd1 mRNA expression due to a solitary long terminal repeat (LTR) in intron 4 of Dhtkd1. This LTR harbors an alternate splice donor site leading to a partial splicing defect and as a consequence decreased total and functional Dhtkd1 mRNA, decreased DHTKD1 protein and α-aminoadipic acidemia. Similarly, C57BL/6J mice have decreased Bckdhb mRNA expression due to an LTR retrotransposon in intron 1 of Bckdhb. This transposable element encodes an alternative exon 1 causing aberrant splicing, decreased total and functional Bckdhb mRNA and decreased BCKDHB protein. Using a targeted metabolomics screen, we also reveal elevated plasma C5-carnitine in 129 substrains. This biochemical phenotype resembles isovaleric acidemia and is caused by an exonic splice mutation in Ivd leading to partial skipping of exon 10 and IVD protein deficiency. In summary, this study identifies three causal variants underlying mild inborn errors of metabolism in commonly used inbred mouse strains.
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Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA; Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Carmen A Argmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Jacob Hagen
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Aaron Bender
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA
| | - Wei Zhang
- Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich CH-8093, Switzerland
| | - Alexis M Bachmann
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA; Mount Sinai Genomics, Inc, One Gustave L Levy Place #1497, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY 10029, USA.
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15
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Biomarker Profiling for Pyridoxine Dependent Epilepsy in Dried Blood Spots by HILIC-ESI-MS. Int J Anal Chem 2018; 2018:2583215. [PMID: 30154848 PMCID: PMC6093012 DOI: 10.1155/2018/2583215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/11/2018] [Accepted: 07/08/2018] [Indexed: 12/01/2022] Open
Abstract
Pyridoxine dependent epilepsy is a condition where the affected infant or child has prolonged seizures (status epilepticus), which are nonresponsive to anticonvulsant therapy but can be treated with pharmacological doses of pyridoxine. If identified earlier and treated prophylactically with pyridoxine, severe brain damage due to seizures can be prevented. Alpha-amino adipic semialdehyde (AASA), piperidine-6-carboxylic acid (P6C), and pipecolic acid (PA) are known biomarkers of pyridoxine dependent epilepsy. We report the development and validation of a hydrophilic interaction liquid chromatography (HILIC) hyphenated with mass spectroscopy for the quantification of the above analytes from dried blood spot samples. The samples were extracted using methanol and analysed on a iHILIC fusion plus column with formic acid buffer (pH 2.5): acetonitrile (20:80) at a flow rate of 0.5 mL/min within 3 minutes. The method demonstrated a LOD of 10 ng/mL, LOQ of 50 ng/mL, linearity of r2 ≥ 0.990, and recovery of 92-101.98% for all analytes. The intra- and interday precision CVs were < 8% and 6%, respectively. Extensive stability studies demonstrated that the analytes were stable in stock solution and in matrix when stored at -80°C. We performed method comparison studies of the developed method with the literature reported method using normal samples and matrix matched spiked samples at pathological concentrations to mimic clinical validity. The Bland-Altman analysis for comparison of the analytical suitability of the method for the biomarkers in healthy and spiked samples with the literature reported method revealed a bias which suggested that the method was comparable. The newly developed method involves no derivatisation and has a simple sample preparation and a low run time enabling it to be easily automated with a high sample throughput in a cost-effective manner.
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High sensitivity HPLC method for determination of the allysine concentration in tissue by use of a naphthol derivative. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1064:7-13. [PMID: 28886479 DOI: 10.1016/j.jchromb.2017.08.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/14/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022]
Abstract
Common to all fibrotic and metastatic diseases is the uncontrollable remodeling of tissue that leads to the accumulation of fibrous connective tissue components such as collagen and elastin. Build-up of fibrous tissue occurs through the cross-linking of collagen or elastin monomers, which is initiated through the oxidation of lysine residues to form α-aminoadipic-δ-semialdehyde (allysine). To provide a measure of the extent of collagen oxidation in disease models of fibrosis or metastasis, a rapid, sensitive HPLC method was developed to quantify the amount of allysine present in tissue. Allysine was reacted with sodium 2-naphthol-7-sulfonate under conditions typically applied for acid hydrolysis of tissues (6M HCl, 110°C, 24h) to prepare AL-NP, a fluorescent bis-naphthol derivative of allysine. High performance liquid chromatography was applied for analysis of allysine content. Under optimal reaction and detection conditions, successful separation of AL-NP was achieved with excellent analytical performance attained. Good linear relationship (R2=0.994) between peak area and concentration for AL-NP was attained for 0.35-175pmol of analyte. A detection limit of 0.02pmol in the standard sample with a 20μL injection was achieved for AL-NP, with satisfactory recovery from 88 to 100% determined. The method was applied in the quantification of allysine in healthy and fibrotic mouse lung tissue, with the fibrotic tissue showing a 2.5 fold increase in the content of allysine.
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Pena IA, MacKenzie A, Van Karnebeek CDM. Current knowledge for pyridoxine-dependent epilepsy: a 2016 update. Expert Rev Endocrinol Metab 2017; 12:5-20. [PMID: 30058881 DOI: 10.1080/17446651.2017.1273107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pyridoxine-dependent epilepsy (PDE) is a rare genetic condition characterized by intractable and recurrent neonatal seizures that are uniquely alleviated by high doses of pyridoxine (vitamin B6). This recessive disease is caused by mutations in ALDH7A1, a gene encoding Antiquitin, an enzyme central to lysine degradation. This results in the pathogenic accumulation of the lysine intermediates Aminoadipate Semialdehyde (AASA) and its cyclic equilibrium form Piperideine-6-carboxylate (P6C) in body fluids; P6C reacts with pyridoxal-5'-phosphate (PLP, the active form of vitamin B6) causing its inactivation and leading to pyridoxine-dependent seizures. While PDE is responsive to pharmacological dosages of pyridoxine, despite lifelong supplementation, neurodevelopment delays are observed in >75% of PDE cases. Thus, adjunct treatment strategies are emerging to both improve seizure control and moderate the delays in cognition. These adjunctive therapies, lysine restriction and arginine supplementation, separately or in combination (with pyridoxine thus termed 'triple therapy'), have shown promising results and are recommended in all PDE patients. Other new therapeutic strategies currently in preclinical phase of study include antisense therapy and substrate reduction therapy. We present here a comprehensive review of current treatment options as well as PDE phenotype, differential diagnosis, current management and views upon the future of PDE research.
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Affiliation(s)
- Izabella Agostinho Pena
- a Children's Hospital of Eastern Ontario (CHEO) Research Institute , Ottawa , ON , Canada
- b Department of Cellular and Molecular Medicine , University of Ottawa , Ottawa , ON , Canada
| | - Alex MacKenzie
- a Children's Hospital of Eastern Ontario (CHEO) Research Institute , Ottawa , ON , Canada
- b Department of Cellular and Molecular Medicine , University of Ottawa , Ottawa , ON , Canada
| | - Clara D M Van Karnebeek
- c Department of Pediatrics, BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics , University of British Columbia , Vancouver BC , Canada
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18
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Mouse lysine catabolism to aminoadipate occurs primarily through the saccharopine pathway; implications for pyridoxine dependent epilepsy (PDE). Biochim Biophys Acta Mol Basis Dis 2017; 1863:121-128. [DOI: 10.1016/j.bbadis.2016.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/11/2016] [Accepted: 09/07/2016] [Indexed: 11/24/2022]
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