1
|
Ciapaite J, van Roermund CWT, Bosma M, Gerrits J, Houten SM, IJlst L, Waterham HR, van Karnebeek CDM, Wanders RJA, Zwartkruis FJT, Jans JJ, Verhoeven-Duif NM. Maintenance of cellular vitamin B 6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein. J Biol Chem 2023; 299:105047. [PMID: 37451483 PMCID: PMC10463200 DOI: 10.1016/j.jbc.2023.105047] [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: 01/30/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Recently, biallelic variants in PLPBP coding for pyridoxal 5'-phosphate homeostasis protein (PLPHP) were identified as a novel cause of early-onset vitamin B6-dependent epilepsy. The molecular function and precise role of PLPHP in vitamin B6 metabolism are not well understood. To address these questions, we used PLPHP-deficient patient skin fibroblasts and HEK293 cells and YBL036C (PLPHP ortholog)-deficient yeast. We showed that independent of extracellular B6 vitamer type (pyridoxine, pyridoxamine, or pyridoxal), intracellular pyridoxal 5'-phosphate (PLP) was lower in PLPHP-deficient fibroblasts and HEK293 cells than controls. Culturing cells with pyridoxine or pyridoxamine led to the concentration-dependent accumulation of pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate (PMP), respectively, suggesting insufficient pyridox(am)ine 5'-phosphate oxidase activity. Experiments utilizing 13C4-pyridoxine confirmed lower pyridox(am)ine 5'-phosphate oxidase activity and revealed increased fractional turnovers of PLP and pyridoxal, indicating increased PLP hydrolysis to pyridoxal in PLPHP-deficient cells. This effect could be partly counteracted by inactivation of pyridoxal phosphatase. PLPHP deficiency had a distinct effect on mitochondrial PLP and PMP, suggesting impaired activity of mitochondrial transaminases. Moreover, in YBL036C-deficient yeast, PLP was depleted and PMP accumulated only with carbon sources requiring mitochondrial metabolism. Lactate and pyruvate accumulation along with the decrease of tricarboxylic acid cycle intermediates downstream of α-ketoglutarate suggested impaired mitochondrial oxidative metabolism in PLPHP-deficient HEK293 cells. We hypothesize that impaired activity of mitochondrial transaminases may contribute to this depletion. Taken together, our study provides new insights into the pathomechanisms of PLPBP deficiency and reinforces the link between PLPHP function, vitamin B6 metabolism, and mitochondrial oxidative metabolism.
Collapse
Affiliation(s)
- Jolita Ciapaite
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Carlo W T van Roermund
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Marjolein Bosma
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Johan Gerrits
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lodewijk IJlst
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans R Waterham
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Clara D M van Karnebeek
- United for Metabolic Diseases, The Netherlands; Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands; Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ronald J A Wanders
- United for Metabolic Diseases, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | - Fried J T Zwartkruis
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Judith J Jans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Nanda M Verhoeven-Duif
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands; United for Metabolic Diseases, The Netherlands
| |
Collapse
|
2
|
İpek R, Çavdartepe BE, Kor D, Okuyaz Ç. Pyridoxine-dependent Epilepsy caused by a Novel homozygous mutation in PLPBP Gene. Metab Brain Dis 2022; 37:3027-3032. [PMID: 36308585 DOI: 10.1007/s11011-022-01085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/13/2022] [Indexed: 10/31/2022]
Abstract
Seizures in newborn infants may be the first finding of hereditary metabolic diseases. Pyridoxine-dependent epilepsy (PDE) is a treatable disorder associated with defects in the one of ALDH7A1, PNPO, or PLPBP genes and it is uncommon but progresses with persistent seizures in the neonatal and infancy period. The seizures are generally resistant to traditional antiepileptic drugs and show a dramatic response to high-dose pyridoxine. In 2016, mutations were reported in PLPBP (previously known as PROSC) gene, which encodes pyridoxal phosphate homeostatic protein (PLPHP).When early-onset antiepileptic resistant seizures are not treated, clinical findings emerge including the development of encephalopathy, congenital microcephaly, and subsequent retardation of psychomotor development. The present case is a 33-month-old female infant with seizures starting from postnatal day 1, who did not respond to traditional anti-epileptic drugs but responded to pyridoxine treatment. In the genetic tests, homozygote c.695 C > T (p.Ala232Val) mutation was determined in the PLPBP gene, which has not been previously identified. Since a specific treatment was found, this case is reported with the aim of emphasizing the need to consider pyridoxine dependence, which is one of the vitamin-dependent metabolic encephalopathies, in the differential diagnosis of epilepsy patients.
Collapse
Affiliation(s)
- Rojan İpek
- Department of Pediatric Neurology, Adıyaman Training and Research Hospital, Adıyaman, Turkey.
| | - Büşra Eser Çavdartepe
- Department of Pediatric Neurology, Adıyaman Training and Research Hospital, Adıyaman, Turkey
| | - Deniz Kor
- Department of Child Nutrition and Metabolism Diseases, Çukurova University, Adana, Turkey
| | - Çetin Okuyaz
- Department of Pediatric Neurology, Mersin University, Mersin, Turkey
| |
Collapse
|
3
|
Tramonti A, Ghatge MS, Babor JT, Musayev FN, di Salvo ML, Barile A, Colotti G, Giorgi A, Paredes SD, Donkor AK, Al Mughram MH, de Crécy‐Lagard V, Safo MK, Contestabile R. Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability. Protein Sci 2022; 31:e4471. [PMID: 36218140 PMCID: PMC9601805 DOI: 10.1002/pro.4471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
The pyridoxal 5'-phosphate (PLP) homeostasis protein (PLPHP) is a ubiquitous member of the COG0325 family with apparently no catalytic activity. Although the actual cellular role of this protein is unknown, it has been observed that mutations of the PLPHP encoding gene affect the activity of PLP-dependent enzymes, B6 vitamers and amino acid levels. Here we report a detailed characterization of the Escherichia coli ortholog of PLPHP (YggS) with respect to its PLP binding and transfer properties, stability, and structure. YggS binds PLP very tightly and is able to slowly transfer it to a model PLP-dependent enzyme, serine hydroxymethyltransferase. PLP binding to YggS elicits a conformational/flexibility change in the protein structure that is detectable in solution but not in crystals. We serendipitously discovered that the K36A variant of YggS, affecting the lysine residue that binds PLP at the active site, is able to bind PLP covalently. This observation led us to recognize that a number of lysine residues, located at the entrance of the active site, can replace Lys36 in its PLP binding role. These lysines form a cluster of charged residues that affect protein stability and conformation, playing an important role in PLP binding and possibly in YggS function.
Collapse
Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia MolecolariConsiglio Nazionale delle RicercheRomeItaly
- Istituto Pasteur Italia‐Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaRomeItaly
| | - Mohini S. Ghatge
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Jill T. Babor
- Department of Microbiology and Cell ScienceUniversity of FloridaGainsvilleFloridaUSA
| | - Faik N. Musayev
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia‐Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaRomeItaly
| | - Anna Barile
- Istituto di Biologia e Patologia MolecolariConsiglio Nazionale delle RicercheRomeItaly
- Istituto Pasteur Italia‐Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaRomeItaly
| | - Gianni Colotti
- Istituto di Biologia e Patologia MolecolariConsiglio Nazionale delle RicercheRomeItaly
| | - Alessandra Giorgi
- Istituto Pasteur Italia‐Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaRomeItaly
| | - Steven D. Paredes
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Akua K. Donkor
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Mohammed H. Al Mughram
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Valérie de Crécy‐Lagard
- Department of Microbiology and Cell ScienceUniversity of FloridaGainsvilleFloridaUSA
- Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Martin K. Safo
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Roberto Contestabile
- Istituto Pasteur Italia‐Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaRomeItaly
| |
Collapse
|
4
|
Alsubhi S, Osterman B, Chrestian N, Dubeau F, Buhas D, Srour M. Case report: PLPHP deficiency, a rare but important cause of B6-responsive disorders: A report of three novel individuals and review of 51 cases. Front Neurol 2022; 13:913652. [PMID: 36324377 PMCID: PMC9618642 DOI: 10.3389/fneur.2022.913652] [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: 04/06/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
PLPHP (pyridoxal-phosphate homeostasis protein) deficiency is caused by biallelic pathogenic variants in PLPBP and is a rare cause of pyridoxine-responsive disorders. We describe three French-Canadian individuals with PLPHP deficiency, including one with unusual paroxysmal episodes lacking EEG correlation with a suspicious movement disorder, rarely reported in B6RDs. In addition, we review the clinical features and treatment responses of all 51 previously published individuals with PLPHP deficiency. Our case series underlines the importance of considering PLPBP mutations in individuals with partially B6-responsive seizures and highlights the presence of a founder effect in the French-Canadian population.
Collapse
Affiliation(s)
- Sarah Alsubhi
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Bradley Osterman
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Nicolas Chrestian
- Department of Pediatric Neurology, Pediatric Neuromuscular Disorder, Centre Mère Enfant Soleil, Laval University, Quebec City, QC, Canada
| | - François Dubeau
- Department of Neurology and Neurosurgery McGill University, Montreal, QC, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Center, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery McGill University, Montreal, QC, Canada
- Child Health and Human Development Program (CHHD), McGill University Health Center Research Institute, Montreal, QC, Canada
- *Correspondence: Myriam Srour
| |
Collapse
|
5
|
The Conserved Family of the Pyridoxal Phosphate-Binding Protein (PLPBP) and Its Cyanobacterial Paradigm PipY. Life (Basel) 2022; 12:life12101622. [PMID: 36295057 PMCID: PMC9605639 DOI: 10.3390/life12101622] [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: 09/20/2022] [Revised: 10/05/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
The PLPBP family of pyridoxal phosphate-binding proteins has a high degree of sequence conservation and is represented in all three domains of life. PLPBP members, of which a few representatives have been studied in different contexts, are single-domain proteins with no known enzymatic activity that exhibit the fold type III of PLP-holoenzymes, consisting in an α/β barrel (TIM-barrel), where the PLP cofactor is solvent-exposed. Despite the constant presence of cofactor PLP (a key catalytic element in PLP enzymes), PLPBP family members appear to have purely regulatory functions affecting the homeostasis of vitamin B6 vitamers and amino/keto acids. Perturbation of these metabolites and pleiotropic phenotypes have been reported in bacteria and zebrafish after PLPBP gene inactivation as well as in patients with vitamin B6-dependent epilepsy that results from loss-of-function mutations at the PLPBP. Here, we review information gathered from diverse studies and biological systems, emphasizing the structural and functional conservation of the PLPBP members and discussing the informative nature of model systems and experimental approaches. In this context, the relatively high level of structural and functional characterization of PipY from Synechococcus elongatus PCC 7942 provides a unique opportunity to investigate the PLPBP roles in the context of a signaling pathway conserved in cyanobacteria.
Collapse
|
6
|
Ito T. Role of the conserved pyridoxal 5'-phosphate-binding protein YggS/PLPBP in vitamin B6 and amino acid homeostasis. Biosci Biotechnol Biochem 2022; 86:1183-1191. [PMID: 35803498 DOI: 10.1093/bbb/zbac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022]
Abstract
The YggS/PLPBP protein (also called COG0325 or PLPHP) is a conserved pyridoxal 5'-phosphate (PLP)-binding protein present in all three domains of life. Recent studies have demonstrated that disruption or mutation of this protein has multifaceted effects in various organisms, including vitamin B6-dependent epilepsy in humans. In Escherichia coli, disruption of this protein-encoded by yggS-perturbs Thr-Ile/Val metabolism, one-carbon metabolism, coenzyme A synthesis, and vitamin B6 homeostasis. This protein is critical for maintaining low levels of pyridoxine 5'-phosphate (PNP) in various organisms. In the yggS-deficient E. coli strain, inhibition of PLP-dependent enzymes, such as the glycine cleavage system by PNP is the root cause of metabolic perturbation. Our data suggest that the YggS/PLPBP protein may be involved in the balancing of B6 vitamers by mediating efficient turnover of protein-bound B6 vitamers. This paper reviews recent findings on the function of the YggS/PLPBP protein.
Collapse
Affiliation(s)
- Tomokazu Ito
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi, Japan
| |
Collapse
|
7
|
Mechanism of pyridoxine 5'-phosphate accumulation in PLPBP protein-deficiency. J Bacteriol 2022; 204:e0052121. [PMID: 34978460 DOI: 10.1128/jb.00521-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pyridoxal 5'-phosphate (PLP)-binding protein (PLPBP) plays an important role in vitamin B6 homeostasis. Loss of this protein in organisms such as Escherichia coli and humans disrupts the vitamin B6 pool and induces intracellular accumulation of pyridoxine 5'-phosphate (PNP), which is normally undetectable in wild-type cells. The accumulated PNP could affect diverse metabolic systems through inhibition of some PLP-dependent enzymes. In this study, we investigated the as yet unclear mechanism of intracellular accumulation of PNP by the loss of PLPBP protein encoded by yggS in E. coli. Genetic studies using several PLPBP-deficient strains of E. coli lacking known enzyme(s) in the de novo or salvage pathway of vitamin B6, which includes pyridoxine (amine) 5'-phosphate oxidase (PNPO), PNP synthase, pyridoxal kinase, and pyridoxal reductase, demonstrated that neither the flux from the de novo pathway nor the salvage pathway solely contributed to the PNP accumulation caused by the PLPBP mutation. Studies with the strains lacking both PLPBP and PNPO suggested that PNP shares the same pool with PMP, and showed that PNP levels are impacted by PMP levels and vice versa. We show that disruption of PLPBP lead to perturb PMP homeostasis, which may result in PNP accumulation in the PLPBP-deficient strains. Importance A PLP-binding protein PLPBP from the conserved COG0325 family has recently been recognized as a key player in vitamin B6 homeostasis in various organisms. Loss of PLPBP disrupts vitamin B6 homeostasis and perturbs diverse metabolisms, including amino acid and α-keto acid metabolism. Accumulation of PNP is a characteristic phenotype of the PLPBP deficiency and is suggested to be a potential cause of the pleiotropic effects, but the mechanism of the PNP accumulation was poorly understood. In this study, we show that fluxes for PNP synthesis/metabolism are not responsible for the accumulation of PNP. Our results indicate that PLPBP is involved in the homeostasis of pyridoxamine 5'-phosphate, and its disruption may lead to the accumulation of PNP in PLPBP-deficiency.
Collapse
|
8
|
Pyridoxal and α-ketoglutarate independently improve function of Saccharomyces cerevisiae Thi5 in the metabolic network of Salmonella enterica. J Bacteriol 2021; 204:e0045021. [PMID: 34662241 DOI: 10.1128/jb.00450-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial metabolism is often considered modular, but metabolic engineering studies have shown that transferring pathways, or modules, between organisms is not always straightforward. The Thi5-dependent pathway(s) for synthesis of the pyrimidine moiety of thiamine from Saccharomyces cerevisiae and Legionella pneumophila functioned differently when incorporated into the metabolic network of Salmonella enterica. Function of Thi5 from Saccharomyces cerevisiae (ScThi5) required modification of the underlying metabolic network, while LpThi5 functioned with the native network. Here we probe the metabolic requirements for heterologous function of ScThi5 and report a strong genetic and physiological evidence for a connection between alpha-ketoglutarate (αKG) levels and ScThi5 function. The connection was built with two classes of genetic suppressors linked to metabolic flux or metabolite pool changes. Further, direct modulation of nitrogen assimilation through nutritional or genetic modification implicated αKG levels in Thi5 function. Exogenous pyridoxal similarly improved ScThi5 function in S. enterica. Finally, directly increasing αKG and PLP with supplementation improved function of both ScThi5 and relevant variants of Thi5 from Legionella pneumophila (LpThi5). The data herein suggest structural differences between ScThi5 and LpThi5 impact their level of function in vivo and implicate αKG in supporting function of the Thi5 pathway when placed in the heterologous metabolic network of S. enterica. IMPORTANCE Thiamine biosynthesis is a model metabolic node that has been used to extend our understanding of metabolic network structure and individual enzyme function. The requirements for in vivo function of the Thi5-dependent pathway found in Legionella and yeast are poorly characterized. Here we suggest that αKG modulates function of the Thi5 pathway in S. enterica and provide evidence that structural variation between ScThi5 and LpThi5 contribute to their functional differences in a Salmonella enterica host.
Collapse
|
9
|
Myers KA, Scheffer IE. Precision Medicine Approaches for Infantile-Onset Developmental and Epileptic Encephalopathies. Annu Rev Pharmacol Toxicol 2021; 62:641-662. [PMID: 34579535 DOI: 10.1146/annurev-pharmtox-052120-084449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epilepsy is an etiologically heterogeneous condition; however, genetic factors are thought to play a role in most patients. For those with infantile-onset developmental and epileptic encephalopathy (DEE), a genetic diagnosis is now obtained in more than 50% of patients. There is considerable motivation to utilize these molecular diagnostic data to help guide treatment, as children with DEEs often have drug-resistant seizures as well as developmental impairment related to cerebral epileptiform activity. Precision medicine approaches have the potential to dramatically improve the quality of life for these children and their families. At present, treatment can be targeted for patients with diagnoses in many genetic causes of infantile-onset DEE, including genes encoding sodium or potassium channel subunits, tuberous sclerosis, and congenital metabolic diseases. Precision medicine may refer to more intelligent choices of conventional antiseizure medications, repurposed agents previously used for other indications, novel compounds, enzyme replacement, or gene therapy approaches. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Kenneth A Myers
- Research Institute of the McGill University Health Centre, Division of Child Neurology, Department of Pediatrics, and Department of Neurology and Neurosurgery, Montreal Children's Hospital, McGill University, Montreal, Quebec H4A 3J1, Canada;
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria 3084, Australia; .,Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Parkville, Victoria 3052, Australia.,The Florey Institute of Neuroscience and Mental Health and Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
| |
Collapse
|
10
|
Vu HN, Downs DM. Loss of YggS (COG0325) impacts aspartate metabolism in Salmonella enterica. Mol Microbiol 2021; 116:1232-1240. [PMID: 34498310 DOI: 10.1111/mmi.14810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022]
Abstract
YggS is a pyridoxal 5'-phosphate (PLP)-binding protein of the conserved COG0325 family. Despite a connection with vitamin B6 homeostasis in many species, neither a precise biochemical activity nor the molecular mechanism of how YggS contributes to cellular function has been described. In a transposon mutagenesis screen, we found that insertions in aspC (encoding a PLP-dependent aspartate aminotransferase, EC 2.6.1.1) in a Salmonella enterica strain lacking yggS caused a synthetic growth defect, which could be rescued by the addition of exogenous aspartate. Characterization of spontaneous suppressors which improved the growth of the yggS aspC double mutant suggested that this synthetic aspartate limitation was dependent on TyrB, a PLP-dependent aromatic amino acid aminotransferase (EC 2.6.1.57). Genetic and biochemical data were consistent with the hypothesis that TyrB activity was inhibited by accumulated pyridoxine 5'-phosphate and α-keto acids caused by a yggS mutation. This study provides data consistent with a working model implicating YggS in modulating concentrations of B6 vitamers via transamination.
Collapse
Affiliation(s)
- Huong N Vu
- Department of Microbiology, The University of Georgia, Athens, Georgia, USA
| | - Diana M Downs
- Department of Microbiology, The University of Georgia, Athens, Georgia, USA
| |
Collapse
|
11
|
Pal M, Lace B, Labrie Y, Laflamme N, Rioux N, Setty ST, Dugas M, Gosselin L, Droit A, Chrestian N, Rivest S. A founder mutation in the PLPBP gene in families from Saguenay-Lac-St-Jean region affected by a pyridoxine-dependent epilepsy. JIMD Rep 2021; 59:32-41. [PMID: 33977028 PMCID: PMC8100403 DOI: 10.1002/jmd2.12196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022] Open
Abstract
Pyridoxine-dependent epilepsy (PDE) is a relatively rare subgroup of epileptic disorders. They generally present in infancy as an early onset epileptic encephalopathy or seizures, refractory to standard treatments, with rapid and variable responses to vitamin B6 treatment. Whole exome sequencing of three unrelated families identified homozygous pathogenic mutation c.370_373del, p.Asp124fs in PLPBP gene in five persons. Haplotype analysis showed a single shared profile for the affected persons and their parents, leading to a hypothesis about founder effect of the mutation in Saguenay-Lac-St-Jean region of French Canadians. All affected probands also shared one single mitochondrial haplotype T2b3 and two rare variations in the mitochondrial genome m.801A>G and m.5166A>G suggesting that a single individual female introduced PLPBP mutation c.370_373del, p.Asp124fs in Quebec. The mutation p.Asp124fs causes a severe disease phenotype with delayed myelination and cortical/subcortical brain atrophy. The most noteworthy radiological finding in this Quebec founder mutation is the presence of the temporal cysts that can be used as a marker of the disease. Also, both patients, who are alive, had a history of prenatal supplements taken by their mothers as antiemetic medication with high doses of pyridoxine. In the context of suspected PDE in patients with neonatal refractory seizures, treatment with pyridoxine and/or Pyridoxal-5-phophate has to be started immediately and continued until the results of genetic analysis received. Even with early appropriate treatment, neurological outcome of our patient is still poor.
Collapse
Affiliation(s)
- Maitou Pal
- Faculty of MedicineLaval UniversityQuébecQuébecCanada
| | - Baiba Lace
- Department of Medical GeneticsCentre Mère Enfant Soleil, Laval UniversityQuébecQuébecCanada
| | - Yvan Labrie
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Nathalie Laflamme
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Nadie Rioux
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Samarth Thonta Setty
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Marc‐Andre Dugas
- Department of PediatricsCentre Mère Enfant Soleil, Laval UniversityQuébecQuébecCanada
| | - Louise Gosselin
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Arnaud Droit
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| | - Nicolas Chrestian
- Department of Pediatric Neurology, Pediatric Neuromuscular DisorderCentre Mère Enfant Soleil, Laval UniversityQuébecQuébecCanada
| | - Serge Rivest
- Centre de recherche CHU de Québec‐ Université Laval, Laval UniversityQuébecQuébecCanada
| |
Collapse
|
12
|
Espinoza AC, Wright MA, Candee MS, Trandafir C, Nelson GR. Child Neurology: Late-Onset Vitamin B 6-Dependent Epilepsy Identified by Rapid Genome Sequencing. Neurology 2021; 96:911-914. [PMID: 33766999 DOI: 10.1212/wnl.0000000000011891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- A Chris Espinoza
- From the Department of Pediatrics, Division of Pediatric Neurology, University of Utah, Salt Lake City. Cristina Trandafir is currently at Baylor College of Medicine, Houston, TX.
| | - Melissa A Wright
- From the Department of Pediatrics, Division of Pediatric Neurology, University of Utah, Salt Lake City. Cristina Trandafir is currently at Baylor College of Medicine, Houston, TX
| | - Meghan S Candee
- From the Department of Pediatrics, Division of Pediatric Neurology, University of Utah, Salt Lake City. Cristina Trandafir is currently at Baylor College of Medicine, Houston, TX
| | - Cristina Trandafir
- From the Department of Pediatrics, Division of Pediatric Neurology, University of Utah, Salt Lake City. Cristina Trandafir is currently at Baylor College of Medicine, Houston, TX
| | - Gary R Nelson
- From the Department of Pediatrics, Division of Pediatric Neurology, University of Utah, Salt Lake City. Cristina Trandafir is currently at Baylor College of Medicine, Houston, TX
| |
Collapse
|
13
|
Heath O, Pitt J, Mandelstam S, Kuschel C, Vasudevan A, Donoghue S. Early-onset vitamin B 6-dependent epilepsy due to pathogenic PLPBP variants in a premature infant: A case report and review of the literature. JIMD Rep 2021; 58:3-11. [PMID: 33728241 PMCID: PMC7932866 DOI: 10.1002/jmd2.12183] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 01/17/2023] Open
Abstract
Vitamin B6-dependent epilepsies are a heterogeneous group of disorders characterized by decreased availability of the active cofactor pyridoxal-5'-phosphate (PLP). While pathogenic variants in ALDH7A1 or PNPO genes account for most cases of these disorders, biallelic pathogenic variants in PLPBP have been shown to cause a form of early onset vitamin B6-dependent epilepsy (EPVB6D). PLPBP is thought to play a role in the homeostatic regulation of vitamin B6, by supplying PLP to apoenzymes while limiting side-reaction toxicity related to excess unbound PLP. Neonatal-onset intractable seizures that respond to pyridoxine and/or PLP are a predominant feature of EPVB6D in humans. Unlike other causes of vitamin B6-dependent epilepsies; however, a specific biomarker for this disorder has yet to be identified. Here we present data from a premature infant found to have pathogenic variants in PLPBP and propose that prematurity may provide an additional clue for early consideration of this diagnosis. We discuss these findings in context of previously published genotypic, phenotypic, and metabolic data from similarly affected patients.
Collapse
Affiliation(s)
- Oliver Heath
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
| | - James Pitt
- Department of Biochemical Genetics, Victorian Clinical Genetics ServiceMurdoch Children's Research InstituteMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - Simone Mandelstam
- Department of Medical ImagingThe Royal Children's Hospital and Murdoch Children's Research InstituteMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
- Department of RadiologyUniversity of MelbourneMelbourneAustralia
| | - Carl Kuschel
- Department of Obstetrics and GynecologyThe Royal Women's HospitalMelbourneAustralia
| | - Anand Vasudevan
- Department of GeneticsThe Royal Women's HospitalMelbourneAustralia
| | - Sarah Donoghue
- Department of Metabolic MedicineThe Royal Children's HospitalMelbourneAustralia
- Department of Biochemical Genetics, Victorian Clinical Genetics ServiceMurdoch Children's Research InstituteMelbourneAustralia
| |
Collapse
|
14
|
Ahmed S, DeBerardinis RJ, Ni M, Afroze B. Vitamin B6-dependent epilepsy due to pyridoxal phosphate-binding protein (PLPBP) defect - First case report from Pakistan and review of literature. Ann Med Surg (Lond) 2020; 60:721-727. [PMID: 33425341 PMCID: PMC7779953 DOI: 10.1016/j.amsu.2020.11.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 11/28/2020] [Accepted: 11/28/2020] [Indexed: 11/16/2022] Open
Abstract
Introduction The Vitamin B6-dependent epilepsies are a heterogeneous group of autosomal recessive disorders usually characterized by neonatal onset seizures responsive to treatment with vitamin B6 available as pyridoxine (PN) or as the biologically active form pyridoxal 5-phosphate (PLP). The vitamin B6–dependent epilepsies are caused by mutations in at least five different genes involved in B6 metabolism. A literature review revealed that only 30 patients with vitamin B6-dependent epilepsy caused by PLPBP mutation have been reported worldwide. Presentation of case We report a case of baby boy born to first-cousin Pakistani parents who presented with generalized as well as focal seizures starting a few hours after birth and responsive to PLP. Whole exome sequencing revealed a homozygous pathogenic variant NM_007198.4:c.46_47insCA, NP_009129.1:p.Leu17Hisfs, causing a CA duplication resulting in a frameshift in the PLPBP gene. Discussion Vitamin B6-Dependent Epilepsy due to PLPBP defect is a rare disorder. The developmental outcomes are variable even with early therapy. Few patients are reported to achieve optimal developmental milestones with therapy. PLP has been advocated as the treatment of choice for PLPBP defect, but oral PN has also demonstrated good seizure control in some patients, including ours. Conclusion Vitamin B6-dependent epilepsy due to PLPBP defect is an important differential diagnosis to consider in patients with biochemical features suggestive of pyridoxamine 5′-phosphate Oxidase (PNPO) defect and gene testing can facilitate in reaching the correct diagnosis. Prompt diagnosis and treatment led to excellent seizure control in most patients. The Vitamin B6-dependent epilepsies are a heterogeneous group of autosomal recessive disorders. A literature review revealed that only 30 patients with PLPBP mutation have been reported. We report a case of baby boy born to first-cousin Pakistani parents responsive to pyridoxal 5-phosphate.
Collapse
Affiliation(s)
- Sibtain Ahmed
- Section of Clinical Chemistry, Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute at UT Southwestern, Texas, USA, Howard Hughes Medical Institute, UT Southwestern Medical Center, USA
| | - Min Ni
- Children's Medical Center Research Institute at UT Southwestern, Texas, USA
| | - Bushra Afroze
- Department of Paediatrics & Child Health, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| |
Collapse
|
15
|
Akiyama T, Hyodo Y, Hasegawa K, Oboshi T, Imai K, Ishihara N, Dowa Y, Koike T, Yamamoto T, Shibasaki J, Shimbo H, Fukuyama T, Takano K, Shiraku H, Takeshita S, Okanishi T, Baba S, Kubota M, Hamano SI, Kobayashi K. Pyridoxal in the Cerebrospinal Fluid May Be a Better Indicator of Vitamin B6-dependent Epilepsy Than Pyridoxal 5'-Phosphate. Pediatr Neurol 2020; 113:33-41. [PMID: 32980745 DOI: 10.1016/j.pediatrneurol.2020.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND We aimed to demonstrate the biochemical characteristics of vitamin B6-dependent epilepsy, with a particular focus on pyridoxal 5'-phosphate and pyridoxal in the cerebrospinal fluid. METHODS Using our laboratory database, we identified patients with vitamin B6-dependent epilepsy and extracted their data on the concentrations of pyridoxal 5'-phosphate, pyridoxal, pipecolic acid, α-aminoadipic semialdehyde, and monoamine neurotransmitters. We compared the biochemical characteristics of these patients with those of other epilepsy patients with low pyridoxal 5'-phosphate concentrations. RESULTS We identified seven patients with pyridoxine-dependent epilepsy caused by an ALDH7A1 gene abnormality, two patients with pyridoxal 5'-phosphate homeostasis protein deficiency, and 28 patients with other epilepsies with low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. Cerebrospinal fluid pyridoxal and pyridoxal 5'-phosphate concentrations were low in patients with vitamin B6-dependent epilepsy but cerebrospinal fluid pyridoxal concentrations were not reduced in most patients with other epilepsies with low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. Increase in 3-O-methyldopa and 5-hydroxytryptophan was demonstrated in some patients with vitamin B6-dependent epilepsy, suggestive of pyridoxal 5'-phosphate deficiency in the brain. CONCLUSIONS Low cerebrospinal fluid pyridoxal concentrations may be a better indicator of pyridoxal 5'-phosphate deficiency in the brain in vitamin B6-dependent epilepsy than low cerebrospinal fluid pyridoxal 5'-phosphate concentrations. This finding is especially helpful in individuals with suspected pyridoxal 5'-phosphate homeostasis protein deficiency, which does not have known biomarkers.
Collapse
Affiliation(s)
- Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kosei Hasegawa
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Taikan Oboshi
- Department of Pediatric Neurology, Osaka Women's and Children's Hospital, Osaka, Japan; Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Katsumi Imai
- Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Aichi, Japan
| | - Yuri Dowa
- Department of Neurology, Gunma Children's Medical Center, Gunma, Japan
| | - Takayoshi Koike
- Department of Pediatrics, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Institute of Clinical Genomics, Tokyo Women's Medical University, Tokyo, Japan
| | - Jun Shibasaki
- Department of Neonatology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Hiroko Shimbo
- Clinical Institute, Kanagawa Children's Medical Center, Kanagawa, Japan
| | | | - Kyoko Takano
- Center for Medical Genetics, Shinshu University Hospital, Nagano, Japan
| | - Hiroshi Shiraku
- Department of Pediatrics, JA Toride Medical Center, Ibaraki, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, Kanagawa, Japan
| | - Tohru Okanishi
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Shizuoka, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Shizuoka, Japan
| | - Masaya Kubota
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Shin-Ichiro Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan; Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| |
Collapse
|
16
|
Jiao X, Xue J, Gong P, Wu Y, Zhang Y, Jiang Y, Yang Z. Clinical and genetic features in pyridoxine-dependent epilepsy: a Chinese cohort study. Dev Med Child Neurol 2020; 62:315-321. [PMID: 31737911 DOI: 10.1111/dmcn.14385] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/18/2023]
Abstract
AIM To characterize the clinical and genetic characteristics of a large cohort of patients with pyridoxine-dependent epilepsy (PDE). METHOD We retrospectively collected clinical and genetic information of 33 (15 males, 18 females; mean [SD] age 4y 11mo [2y 5mo]; 1y 3mo-10y 4mo) patients with PDE from 31 unrelated families at a single centre. RESULTS There were many types of seizures, with focal seizures in 32 cases. Dravet syndrome was suspected clinically in two patients. Electroencephalogram (EEG) was normal in seven patients at the initial stage and then in 17 patients during pyridoxine maintenance therapy. Genetic studies revealed 26 kinds of variants in ALDH7A1 and four in PLPBP with 18 variants unreported previously, and 48 ALDH7A1 variants were located in exon 11, 12, 14, and 17 or intron 9 and 11. In addition, three patients carried different exons deletion. Among these, seizures could be controlled for several years in one patient by levetiracetam monotherapy. Another patient remained seizure free for up to 7 months without therapy. All patients received oral pyridoxine treatment, with only one case (with exon 8-13 deletion) showing poor control. INTERPRETATION This study illustrates the range of clinical presentations and genetic causes in PDE, as well as responsiveness to antiepileptic drugs. A relationship between EEG and pyridoxine therapy could be seen in many cases. Seizure control was seen in all with pyridoxine monotherapy except for one patient. WHAT THIS PAPER ADDS There is a parallel relationship between electroencephalogram and pyridoxine therapy in many patients. Patients with pyridoxine-dependent epilepsy may respond well to low-dose pyridoxine.
Collapse
Affiliation(s)
- Xianru Jiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jiao Xue
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Pan Gong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| |
Collapse
|
17
|
Helbig I, Ellis CA. Personalized medicine in genetic epilepsies - possibilities, challenges, and new frontiers. Neuropharmacology 2020; 172:107970. [PMID: 32413583 DOI: 10.1016/j.neuropharm.2020.107970] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/05/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
Abstract
Identifying the optimal treatment based on specific characteristics of each patient is the main promise of precision medicine. In the field of epilepsy, the identification of more than 100 causative genes provides the enticing possibility of treatments targeted to specific disease etiologies. These conditions include classical examples, such as the use of vitamin B6 in antiquitin deficiency or the ketogenic diet in GLUT1 deficiency, where the disease mechanism can be directly addressed by the selection of a specific therapeutic compound. For epilepsies caused by channelopathies there have been advances in understanding how the selection of existing medications can be targeted to the functional consequences of genetic alterations. We discuss the examples of the use of sodium channel blockers such as phenytoin and oxcarbazepine in the sodium channelopathies, quinidine in KCNT1-related epilepsies, and strategies in GRIN-related epilepsies as examples of epilepsy precision medicine. Assessing the clinical response to targeted treatments of these conditions has been complicated by genetic and phenotypic heterogeneity, as well as by various neurological and non-neurological comorbidities. Moving forward, the development of standardized outcome measures will be critical to successful precision medicine trials in complex and heterogeneous disorders like the epilepsies. Finally, we address new frontiers in epilepsy precision medicine, including the need to match the growing volume of genetic data with high-throughput functional assays to assess the functional consequences of genetic variants and the ability to extract clinical data at large scale from electronic medical records and apply quantitative methods based on standardized phenotyping language.
Collapse
Affiliation(s)
- Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Colin A Ellis
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| |
Collapse
|
18
|
Fux A, Sieber SA. Biochemical and Proteomic Studies of Human Pyridoxal 5'-Phosphate-Binding Protein (PLPBP). ACS Chem Biol 2020; 15:254-261. [PMID: 31825581 PMCID: PMC9558310 DOI: 10.1021/acschembio.9b00857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The pyridoxal 5′-phosphate-binding protein (PLPBP)
is an
evolutionarily conserved protein linked to pyridoxal 5′-phosphate-binding.
Although mutations in PLPBP were shown to cause vitamin B6-dependent
epilepsy, its cellular role and function remain elusive. We here report
a detailed biochemical investigation of human PLPBP and its epilepsy-causing
mutants by evaluating stability, cofactor binding, and oligomerization.
In this context, chemical cross-linking combined with mass spectrometry
unraveled an unexpected dimeric assembly of PLPBP. Furthermore, the
interaction network of PLPBP was elucidated by chemical cross-linking
paired with co-immunoprecipitation. A mass spectrometric analysis
in a PLPBP knockout cell line resulted in distinct proteomic changes
compared to wild type cells, including upregulation of several cytoskeleton-
and cell division-associated proteins. Finally, transfection experiments
with vitamin B6-dependent epilepsy-causing PLPBP variants indicate
a potential role of PLPBP in cell division as well as proper muscle
function. Taken together, our studies on the structure and cellular
role of human PLPBP enable a better understanding of the physiological
and pathological mechanism of this important protein.
Collapse
Affiliation(s)
- Anja Fux
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| |
Collapse
|
19
|
Ito T, Hori R, Hemmi H, Downs DM, Yoshimura T. Inhibition of glycine cleavage system by pyridoxine 5'-phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli. Mol Microbiol 2019; 113:270-284. [PMID: 31677193 DOI: 10.1111/mmi.14415] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
The YggS/Ybl036c/PLPBP family includes conserved pyridoxal 5'-phosphate (PLP)-binding proteins that play a critical role in the homeostasis of vitamin B6 and amino acids. Disruption of members of this family causes pleiotropic effects in many organisms by unknown mechanisms. In Escherichia coli, conditional lethality of the yggS and glyA (encoding serine hydroxymethyltransferase) has been described, but the mechanism of lethality was not determined. Strains lacking yggS and serA (3-phosphoglycerate dehydrogenase) were conditionally lethality in the M9-glucose medium supplemented with Gly. Analyses of vitamin B6 pools found the high-levels of pyridoxine 5'-phosphate (PNP) in the two yggS mutants. Growth defects of the double mutants could be eliminated by overexpressing PNP/PMP oxidase (PdxH) to decrease the PNP levels. Further, a serA pdxH strain, which accumulates PNP in the presence of yggS, exhibited similar phenotype to serA yggS mutant. Together these data suggested the inhibition of the glycine cleavage (GCV) system caused the synthetic lethality. Biochemical assays confirmed that PNP disrupts the GCV system by competing with PLP in GcvP protein. Our data are consistent with a model in which PNP-dependent inhibition of the GCV system causes the conditional lethality observed in the glyA yggS or serA yggS mutants.
Collapse
Affiliation(s)
- Tomokazu Ito
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Ran Hori
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Tohru Yoshimura
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-chou, Chikusa, Nagoya, Aichi, 464-8601, Japan
| |
Collapse
|
20
|
Jensen KV, Frid M, Stödberg T, Barbaro M, Wedell A, Christensen M, Bak M, Ek J, Madsen CG, Darin N, Grønborg S. Diagnostic pitfalls in vitamin B6-dependent epilepsy caused by mutations in the PLPBP gene. JIMD Rep 2019; 50:1-8. [PMID: 31741821 PMCID: PMC6850975 DOI: 10.1002/jmd2.12063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/03/2022] Open
Abstract
Vitamin B6-responsive epilepsies are a group of genetic disorders including ALDH7A1 deficiency, PNPO deficiency, and others, usually causing neonatal onset seizures resistant to treatment with common antiepileptic drugs. Recently, biallelic mutations in PLPBP were shown to be a novel cause of vitamin B6-dependent epilepsy with a variable phenotype. The different vitamin B6-responsive epilepsies can be detected and distinguished by their respective biomarkers and genetic analysis. Unfortunately, metabolic biomarkers for early detection and prognosis of PLPBP deficiency are currently still lacking. Here, we present data from two further patients with vitamin B6-dependent seizures caused by variants in PLPBP, including a novel missense variant, and compare their genotype and phenotypic presentation to previously described cases. Hyperglycinemia and hyperlactatemia are the most consistently observed biochemical abnormalities in pyridoxal phosphate homeostasis protein (PLPHP) deficient patients and were present in both patients in this report within the first days of life. Lactic acidemia, the neuroradiological, and clinical presentation led to misdiagnosis of a mitochondrial encephalopathy in two previously published cases with an early fatal course. Similarly, on the background of glycine elevation in plasma, glycine encephalopathy was wrongly adopted as diagnosis for a patient in our report. In this regard, lactic acidemia as well as hyperglycinemia appear to be diagnostic pitfalls in patients with vitamin B6-responsive epilepsies, including PLPHP deficiency. SYNOPSIS In vitamin B6-responsive epilepsies, including PLPHP deficiency, there are several diagnostic pitfalls, including lactic acidemia as well as hyperglycinemia, highlighting the importance of a pyridoxine trial, and genetic testing.
Collapse
Affiliation(s)
| | - Maria Frid
- Department of PaediatricsRyhov County HospitalJönköpingSweden
| | - Tommy Stödberg
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Neuropaediatric UnitKarolinska University HospitalStockholmSweden
| | - Michela Barbaro
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Anna Wedell
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
- Department of Molecular Medicine and SurgeryScience for Life Laboratory, Karolinska InstitutetStockholmSweden
| | - Mette Christensen
- Department of Clinical GeneticsCopenhagen University HospitalCopenhagenDenmark
| | - Mads Bak
- Department of Clinical GeneticsCopenhagen University HospitalCopenhagenDenmark
| | - Jakob Ek
- Department of Clinical GeneticsCopenhagen University HospitalCopenhagenDenmark
| | - Camilla Gøbel Madsen
- Department of Radiology, Centre for Functional and Diagnostic Imaging and ResearchCopenhagen University, Hvidovre HospitalHvidovreDenmark
| | - Niklas Darin
- Department of PediatricsUniversity of Gothenburg, Sahlgrenska University HospitalGothenburgSweden
| | - Sabine Grønborg
- Department of Clinical GeneticsCopenhagen University HospitalCopenhagenDenmark
- Centre for Inherited Metabolic Diseases, Department of PaediatricsCopenhagen University HospitalCopenhagenDenmark
| |
Collapse
|
21
|
Abstract
Introduction: Vitamin B6 dependent epilepsies are a group of treatable diseases (ALDH7A1 deficiency, PNPO deficiency, PLP binding protein deficiency, hyperprolinaemia type II and hypophosphatasia and glycosylphosphatidylinositol anchor synthesis defects) responding to pyridoxine or pyridoxal-5I-phosphate. Areas covered: A critical review was conducted on the therapeutic management of all the reported patients with genetically confirmed diagnoses of diseases affecting vitamin B6 metabolism and presenting with pyridoxine or pyridoxal-5I-phosphate dependent-seizures. Data about safety and efficacy were analyzed as well as the management of supplementation with pyridoxine or pyridoxal-5I-phosphate both in the acute phases and in the maintenance therapies. The authors also analyzed alternative therapeutic strategies for ALDH7A1 deficiency (lysine-restricted diet, arginine supplementation, oligonucleotide antisense therapy, upstream inhibition of aminoadipic semialdehyde synthase). Expert opinion: The administration of pyridoxine or pyridoxal-5I-phosphate should be considered in all intractable seizures also beyond the first year of life. Lysine restricted diet and arginine supplementation should be introduced in all the confirmed ALDH7A1 deficient patients. Pre or post-natal supplementation with pyridoxine should be given in familial cases until an eventual molecular genetic disconfirmation. Minor data about alternative therapies are available for other disorders of vitamin B6 metabolism.
Collapse
Affiliation(s)
- Mario Mastrangelo
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome , Roma , Italy
| | - Serena Cesario
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome , Roma , Italy
| |
Collapse
|
22
|
Wilson MP, Plecko B, Mills PB, Clayton PT. Disorders affecting vitamin B 6 metabolism. J Inherit Metab Dis 2019; 42:629-646. [PMID: 30671974 DOI: 10.1002/jimd.12060] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022]
Abstract
Vitamin B6 is present in our diet in many forms, however, only pyridoxal 5'-phosphate (PLP) can function as a cofactor for enzymes. The intestine absorbs nonphosphorylated B6 vitamers, which are converted by specific enzymes to the active PLP form. The role of PLP is enabled by its reactive aldehyde group. Pathways reliant on PLP include amino acid and neurotransmitter metabolism, folate and 1-carbon metabolism, protein and polyamine synthesis, carbohydrate and lipid metabolism, mitochondrial function and erythropoiesis. Besides the role of PLP as a cofactor B6 vitamers also play other cellular roles, for example, as antioxidants, modifying expression and action of steroid hormone receptors, affecting immune function, as chaperones and as an antagonist of Adenosine-5'-triphosphate (ATP) at P2 purinoceptors. Because of the vital role of PLP in neurotransmitter metabolism, particularly synthesis of the inhibitory transmitter γ-aminobutyric acid, it is not surprising that various inborn errors leading to PLP deficiency manifest as B6 -responsive epilepsy, usually of early onset. This includes pyridox(am)ine phosphate oxidase deficiency (a disorder affecting PLP synthesis and recycling), disorders affecting PLP import into the brain (hypophosphatasia and glycosylphosphatidylinositol anchor synthesis defects), a disorder of an intracellular PLP-binding protein (PLPBP, previously named PROSC) and disorders where metabolites accumulate that inactivate PLP, for example, ALDH7A1 deficiency and hyperprolinaemia type II. Patients with these disorders can show rapid control of seizures in response to either pyridoxine and/or PLP with a lifelong dependency on supraphysiological vitamin B6 supply. The clinical and biochemical features of disorders leading to B6 -responsive seizures and the treatment of these disorders are described in this review.
Collapse
Affiliation(s)
- Matthew P Wilson
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Barbara Plecko
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, University Childrens' Hospital Graz, Medical University Graz, Graz, Austria
| | - Philippa B Mills
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Peter T Clayton
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| |
Collapse
|
23
|
Ishikawa N, Tateishi Y, Tani H, Kobayashi Y, Itai T, Miyatake S, Kato M, Matsumoto N, Kobayashi M. Successful treatment of intractable life-threatening seizures with perampanel in the first case of early myoclonic encephalopathy with a novel de novo SCN1A mutation. Seizure 2019; 71:20-23. [PMID: 31176277 DOI: 10.1016/j.seizure.2019.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/29/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Early myoclonic encephalopathy (EME) is a form of developmental and epileptic encephalopathy with myoclonic seizures and a suppression burst on electroencephalogram, which occurs during the neonatal or early infantile period and is characterized by highly intractable seizures and severe development impairment. Although multiple genetic aetiologies of EME have been identified, no SCN1A mutation has been reported. METHODS We described a female patient with EME due to an SCN1A mutation. RESULTS She developed frequent myoclonic and apnoeic seizures during the neonatal period. As her seizures were refractory to many antiepileptic drugs, she underwent a tracheotomy and has since been treated with continuous mechanical ventilation. Eventually, perampanel was added, which resulted in the cessation of the apnoeic seizures. Genetic analysis revealed a heterozygous de novo missense mutation in the SCN1A gene (c.2588 T > C:p.Leu863Ser). CONCLUSION This is the first patient with EME due to anSCN1A mutation to be successfully treated with perampanel. Recently, perampanel was reported to be effective in treating Dravet syndrome, including cases with an SCN1A mutation. Perampanel may contribute to seizure reduction in patients with intractable epilepsy carrying the SCN1A mutation.
Collapse
Affiliation(s)
| | - Yuichi Tateishi
- Department of Pediatrics, Hiroshima University Hospital, Japan
| | - Hiroo Tani
- Department of Pediatrics, Hiroshima University Hospital, Japan
| | | | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Hospital, Japan
| |
Collapse
|
24
|
Johannsen J, Bierhals T, Deindl P, Hecher L, Hermann K, Hempel M, Kloth K, Denecke J. Excessive Seizure Clusters in an Otherwise Well-Controlled Epilepsy as a Possible Hallmark of Untreated Vitamin B6-Responsive Epilepsy due to a Homozygous PLPBP Missense Variant. J Pediatr Genet 2019; 8:222-225. [PMID: 31687261 DOI: 10.1055/s-0039-1685501] [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] [Received: 12/25/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Recently, mutations in the PLPBP gene were described as a novel cause for vitamin B6-responsive epilepsy. We report the outcome in case of a male adolescent with a novel homozygous missense variant in PLPBP who was never treated with pyridoxine until the age of 16 years. He presented with only mild cognitive impairment and an early-onset, well-controlled epilepsy. In our patient, excessive seizure clusters and anxiety states occurred intermittently, suggesting that the combination might be a hallmark in untreated patients. Thus, mutations in PLPBP should be addressed even in adolescent patients with only mild learning disabilities and relatively good seizure control over the years.
Collapse
Affiliation(s)
- Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Deindl
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Hecher
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Hermann
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|