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Jasinge E, Fernando M, Indika NLR, Ratnayake PD, Gamaathige N, Ratnaranjith R, Schroeder S, Jones P, Volha S, Jayasena S, Gunaratna AV, Bandara Ekanayake AN, Rolfs A. Clinical, biochemical, and molecular profiles of three Sri Lankan neonates with pyruvate carboxylase deficiency. ADVANCES IN LABORATORY MEDICINE 2024; 5:205-212. [PMID: 38939194 PMCID: PMC11206181 DOI: 10.1515/almed-2023-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/04/2023] [Indexed: 06/29/2024]
Abstract
Objectives Pyruvate carboxylase, a mitochondrial enzyme, catalyses the conversion of glycolytic end-product pyruvate to tricarboxylic acid cycle intermediate, oxaloacetate. Rare pyruvate carboxylase deficiency manifests in three clinical and biochemical phenotypes: neonatal onset type A, infantile onset type B and a benign C type. The objective of this case series is to expand the knowledge of overlapping clinical and biochemical phenotypes of pyruvate carboxylase deficiency. Case presentation We report three Sri Lankan neonates including two siblings, of two unrelated families with pyruvate carboxylase deficiency. All three developed respiratory distress within the first few hours of birth. Two siblings displayed typical biochemical findings reported in type B. The other proband with normal citrulline, lysine, moderate lactate, paraventricular cystic lesions, bony deformities, and a novel missense, homozygous variant c.2746G>C [p.(Asp916His)] in the PC gene, biochemically favoured type A. Conclusions Our findings indicate the necessity of prompt laboratory investigations in a tachypneic neonate with coexisting metabolic acidosis, as early recognition is essential for patient management and family counselling. Further case studies are required to identify overlapping symptoms and biochemical findings in different types of pyruvate carboxylase deficiency phenotypes.
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Affiliation(s)
- Eresha Jasinge
- Department of Chemical Pathology, Lady Ridgeway Hospital for Children, Colombo 8, Sri Lanka
| | - Mihika Fernando
- Department of Chemical Pathology, Lady Ridgeway Hospital for Children, Colombo 8, Sri Lanka
| | - Neluwa-Liyanage Ruwan Indika
- Department of Chemical Pathology, Lady Ridgeway Hospital for Children, Colombo 8, Sri Lanka
- Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Nalin Gamaathige
- Neonatal Intensive Care Unit, De Soysa Hospital for Women, Colombo 8, Sri Lanka
| | | | | | - Patricia Jones
- Children’s Medical Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Subhashinie Jayasena
- Department of Chemical Pathology, Lady Ridgeway Hospital for Children, Colombo 8, Sri Lanka
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Jasinge E, Fernando M, Indika NLR, Ratnayake PD, Gamaathige N, Ratnaranjith R, Schroeder S, Jones P, Volha S, Jayasena S, Gunaratna AV, Ekanayake ANB, Rolfs A. Perfiles clínicos, bioquímicos y moleculares de tres neonatos de Sri Lanka con déficit de piruvato carboxilasa. ADVANCES IN LABORATORY MEDICINE 2024; 5:213-220. [PMID: 38939210 PMCID: PMC11206187 DOI: 10.1515/almed-2024-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/04/2023] [Indexed: 06/29/2024]
Abstract
Objetivos La piruvato carboxilasa (PC), una enzima mitocondrial, cataliza la conversión de piruvato, producto final de la glucólisis, en oxaloacetato, un intermediario del ciclo del ácido tricarboxílico. El déficit de piruvato carboxilasa, un trastorno raro, se manifiesta en tres fenotipos clínicos y bioquímicos: tipo de inicio neonatal (tipo A), tipo de inicio infantil (tipo B) y un tipo benigno (tipo C). Caso clínico Presentamos el caso de tres neonatos de Sri Lanka, incluidos dos hermanos, de dos familias no emparentadas, con déficit de piruvato carboxilasa (DPC). Los tres desarrollaron dificultad respiratoria en las primeras horas de vida. Los dos hermanos presentaron las alteraciones bioquímicas típicas del tipo B. El tercer neonato presentaba niveles normales de citrulina y lisina, niveles moderados de lactato, lesiones quísticas paraventriculares, deformidades óseas y una nueva variante homocigótica sin sentido c.2746G>C [p.(Asp916His)] en el gen PC , indicativos bioquímicos de DPC tipo A. Conclusiones Nuestros hallazgos indican la urgencia de realizar estudios analíticos en los neonatos que presenten taquipnea con acidosis metabólica concomitante, dado que la identificación temprana es crucial para el manejo del paciente y la prestación de consejo genético a la familia. Son necesarios más estudios para identificar los síntomas y alteraciones bioquímicas concurrentes en los diferentes fenotipos de déficit de piruvato carboxilasa.
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Affiliation(s)
- Eresha Jasinge
- Departamento de Patología Química, Hospital Pediátrico Lady Ridgeway, Colombo 8, Sri Lanka
| | - Mihika Fernando
- Departamento de Patología Química, Hospital Pediátrico Lady Ridgeway, Colombo 8, Sri Lanka
| | - Neluwa-Liyanage Ruwan Indika
- Departamento de Patología Química, Hospital Pediátrico Lady Ridgeway, Colombo 8, Sri Lanka
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Nalin Gamaathige
- Unidad de Cuidados Intesivos Neonatales, Hospital Maternal De Soysa Hospital, Colombo 8, Sri Lanka
| | | | | | - Patricia Jones
- Centro médico infantil, Centro médico Southwestern de la Universidad de Texas, Dallas, TX, EEUU
| | | | - Subhashinie Jayasena
- Departamento de Patología Química, Hospital Pediátrico Lady Ridgeway, Colombo 8, Sri Lanka
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Maryami F, Rismani E, Davoudi-Dehaghani E, Khalesi N, Talebi S, Mahdian R, Zeinali S. In silico Analysis of Two Novel Variants in the Pyruvate Carboxylase (PC) Gene Associated with the Severe Form of PC Deficiency. IRANIAN BIOMEDICAL JOURNAL 2023; 27:307-19. [PMID: 37873728 PMCID: PMC10707810 DOI: 10.61186/ibj.27.5.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/17/2023] [Indexed: 12/17/2023]
Abstract
Background Inborne errors of metabolism are a common cause of neonatal death. This study evaluated the acute early-onset metabolic derangement and death in two unrelated neonates. Methods Whole-exome sequencing (WES), Sanger sequencing, homology modeling, and in silico bioinformatics analysis were employed to assess the effects of variants on protein structure and function. Results WES revealed a novel homozygous variant, p.G303Afs*40 and p.R156P, in the pyruvate carboxylase (PC) gene of each neonate, which both were confirmed by Sanger sequencing. Based on the American College of Medical Genetics and Genomics guidelines, the p.G303Afs*40 was likely pathogenic, and the p.R156P was a variant of uncertain significance (VUS). Nevertheless, a known variant at position 156, the p.R156Q, was also a VUS. Protein secondary structure prediction showed changes in p.R156P and p.R156Q variants compared to the wild-type protein. However, p.G303Afs*40 depicted significant changes at C-terminal. Furthermore, comparing the interaction of wild-type and variant proteins with the ATP ligand during simulations, revealed a decreased affinity to the ATP in all the variants. Moreover, analysis of Single nucleotide polymorphism impacts on PC protein using Polyphen-2, SNAP2, FATHMM, and SNPs&GO servers predicted both R156P and R156Q as damaging variants. Likewise, free energy calculations demonstrated the destabilizing effect of both variants on PC. Conclusion This study confirmed the pathogenicity of both variants and suggested them as a cause of type B Pyruvate carboxylase deficiency. The results of this study would provide the family with prenatal diagnosis and expand the variant spectrum in the PC gene,which is beneficial for geneticists and endocrinologists.
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Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children’s Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Reza Mahdian
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Kawsar Human Genetics Research Center, Tehran, Iran
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Gondáš E, Kráľová Trančíková A, Šofranko J, Majerová P, Lučanský V, Dohál M, Kováč A, Murín R. The presence of pyruvate carboxylase in the human brain and its role in the survival of cultured human astrocytes. Physiol Res 2023; 72:403-414. [PMID: 37449752 PMCID: PMC10669001 DOI: 10.33549/physiolres.935026] [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: 10/11/2022] [Accepted: 02/28/2023] [Indexed: 08/26/2023] Open
Abstract
Pyruvate carboxylase (PC) is a mitochondrial, biotin-containing enzyme catalyzing the ATP-dependent synthesis of oxaloacetate from pyruvate and bicarbonate, with a critical anaplerotic role in sustaining the brain metabolism. Based on the studies performed on animal models, PC expression was assigned to be glia-specific. To study PC distribution among human neural cells, we probed the cultured human astrocytes and brain sections with antibodies against PC. Additionally, we tested the importance of PC for the viability of cultured human astrocytes by applying the PC inhibitor 3-chloropropane-1,2-diol (CPD). Our results establish the expression of PC in mitochondria of human astrocytes in culture and brain tissue and also into a subpopulation of the neurons in situ. CPD negatively affected the viability of astrocytes in culture, which could be partially reversed by supplementing media with malate, 2-oxoglutarate, citrate, or pyruvate. The provided data estimates PC expression in human astrocytes and neurons in human brain parenchyma. Furthermore, the enzymatic activity of PC is vital for sustaining the viability of cultured astrocytes.
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Affiliation(s)
- E Gondáš
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
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Lasio MLD, Leshinski AC, Ducich NH, Flore LA, Lehman A, Shur N, Jayakar PB, Hainline BE, Basinger AA, Wilson WG, Diaz GA, Erbe RW, Koeberl DD, Vockley J, Bedoyan JK. Clinical, biochemical and molecular characterization of 12 patients with pyruvate carboxylase deficiency treated with triheptanoin. Mol Genet Metab 2023; 139:107605. [PMID: 37207470 PMCID: PMC10330474 DOI: 10.1016/j.ymgme.2023.107605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Pyruvate carboxylase (PC) deficiency is a rare autosomal recessive mitochondrial neurometabolic disorder of energy deficit resulting in high morbidity and mortality, with limited therapeutic options. The PC homotetramer has a critical role in gluconeogenesis, anaplerosis, neurotransmitter synthesis, and lipogenesis. The main biochemical and clinical findings in PC deficiency (PCD) include lactic acidosis, ketonuria, failure to thrive, and neurological dysfunction. Use of the anaplerotic agent triheptanoin on a limited number of individuals with PCD has had mixed results. We expand on the potential utility of triheptanoin in PCD by examining the clinical, biochemical, molecular, and health-related quality-of-life (HRQoL) findings in a cohort of 12 individuals with PCD (eight with Type A and two each with Types B and C) treated with triheptanoin ranging for 6 days to about 7 years. The main endpoints were changes in blood lactate and HRQoL scores, but collection of useful data was limited to about half of subjects. An overall trend of lactate reduction with time on triheptanoin was noted, but with significant variability among subjects and only one subject reaching close to statistical significance for this endpoint. Parent reported HRQoL assessments with treatment showed mixed results, with some subjects showing no change, some improvement, and some worsening of overall scores. Subjects with buried amino acids in the pyruvate carboxyltransferase domain of PC that undergo destabilizing replacements may be more likely to respond (with lactate reduction or HRQoL improvement) to triheptanoin compared to those with replacements that disrupt tetramerization or subunit-subunit interface contacts. The reason for this difference is unclear and requires further validation. We observed significant variability but an overall trend of lactate reduction with time on triheptanoin and mixed parent reported outcome changes by HRQoL assessments for subjects with PCD on long-term triheptanoin. The mixed results noted with triheptanoin therapy in this study could be due to endpoint data limitation, variability of disease severity between subjects, limitation of the parent reported HRQoL tool, or subject genotype variability. Alternative designed trials and more study subjects with PCD will be needed to validate important observations from this work.
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Affiliation(s)
- M Laura Duque Lasio
- Department of Pathology, University of Utah, Salt Lake City, UT, USA; Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Angela C Leshinski
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nicole H Ducich
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Leigh Anne Flore
- Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit, MI and Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - April Lehman
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit, MI and Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Natasha Shur
- Genetics and Metabolism, Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Parul B Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA
| | - Bryan E Hainline
- Department of Medical and Molecular Genetics, Riley Hospital at Indiana University Health, Indianapolis, IN, USA
| | | | - William G Wilson
- Department of Pediatrics, University of Virginia Health, Charlottesville, VA, USA
| | - George A Diaz
- Division of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard W Erbe
- Departments of Pediatrics and Medicine, University at Buffalo, Buffalo, NY, USA
| | - Dwight D Koeberl
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Jirair K Bedoyan
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Pant P, Chitme H, Sircar R, Prasad R, Prasad HO. Genome-wide association study for single nucleotide polymorphism associated with mural and cumulus granulosa cells of PCOS (polycystic ovary syndrome) and non-PCOS patients. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2023. [DOI: 10.1186/s43094-023-00475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Background
The genetic make-up of local granulosa cells and their function in the pathophysiology of polycystic ovary syndrome (PCOS) is crucial to a full comprehension of the disorder. The major purpose of this study was to compare the Single Nucleotide Polymorphism (SNP) of cumulus granulosa cells (CGCs) and mural granulosa cells (MGCs) between healthy individuals and women with PCOS using genome-wide association analysis (GWA). A case–control study was conducted in a total of 24 women diagnosed with PCOS and 24 healthy non-PCOS women of reproductive age aggregated into 4 samples of 6 patients each. GWA studies entail several processes, such as cell separation, cellular DNA extraction, library preparation followed by interpretation using bioinformatics databases. SNP locations were identified by reference gene also involves the use of Matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry (MS) (MALDI-TOF-MS) for the first sorting. Hybridization with the gene chip was followed by reading the SNP genotypes according to the publications in the literature. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) program and methods were used for GWA studies.
Results
An aggregate of 21,039 SNP calls were obtained from our samples. Genes of autoimmune illnesses, obesity, inflammatory illnesses, nervous system diseases such as retinitis pigmentosa, autism, neural tube defects, and Alzheimer's disease; and various malignancies such as lung cancer, colorectal cancer, breast cancer were also identified in these cells. Gene ranking score reveals that granulosa cells carry key genes of neurological system and reproductive systems especially in brain and testis, respectively.
Conclusions
Mural and Cumulus Granulosa cells were shown to have the PCOS directly and indirectly related genes MMP9, PRKAA2, COMT and HP. We found that the expression of ARID4B, MUC5AC, NID2, CREBBP, GNB1, KIF2C, COL18A1, and HNRNPC by these cells may contribute to PCOS.
Graphical abstract
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7
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Tsygankova P, Bychkov I, Minzhenkova M, Pechatnikova N, Bessonova L, Buyanova G, Naumchik I, Beskorovainiy N, Tabakov V, Itkis Y, Shilova N, Zakharova E. Expanding the genetic spectrum of the pyruvate carboxylase deficiency with novel missense, deep intronic and structural variants. Mol Genet Metab Rep 2022; 32:100889. [PMID: 35782291 PMCID: PMC9240867 DOI: 10.1016/j.ymgmr.2022.100889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Pathogenic variants in the pyruvate carboxylase (PC) gene cause a wide spectrum of recessive phenotypes, ranging from the early-onset fatal encephalopathy to the adult-onset benign form. Results Patient 1 is a 6 y.o. boy with ataxia, hypoglycemia and episodes of lactic acidosis. WGS revealed the novel heterozygous missense variant c.1372A > G (p.Asn458Asp) in the PC gene. Additional analysis revealed discordant reads mapped to chromosomes 11 and 1, so a reciprocal translocation disrupted the PC gene was suspected. The translocation was validated via FISH-analysis and Sanger sequencing of its boundaries. Patient 2 is a 13 y.o. girl with psychomotor delay, episodes of lactic acidosis and ketonuria. WES revealed the novel homozygous intronic variant c.1983-116C > T. The PC's mRNA analysis demonstrated the exonization of several intron 16 sequences and some residual amount of WT mRNA isoform. Two other patients had more severe course of the disease. Their genotype represents missense variants in compound heterozygous and homozygous state (c.1876C > T (p.Arg626Trp), c.2606G > C (p.Gly869Ala), c.2435C > A (p.Ala812Asp). Conclusion In patients with metabolic crises, lactic acidosis and hypoglycemia analysis of PC gene is recommended. WGS with deep bioinformatic analysis should be taken into consideration when none or the only one pathogenic variant in the PC gene is found. In patients with metabolic crises with lactic acidosis and hypoglycemia WGS with deep bioinformatic analysis should be taken when none or the only one heterozygous pathogenic variant in the PC gene is found. PC gene may have more deep intronic pathogenic variants than included in known mutation databases.
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8
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Sheardown E, Mech AM, Petrazzini MEM, Leggieri A, Gidziela A, Hosseinian S, Sealy IM, Torres-Perez JV, Busch-Nentwich EM, Malanchini M, Brennan CH. Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. Neurosci Biobehav Rev 2022; 135:104559. [PMID: 35124155 PMCID: PMC9016269 DOI: 10.1016/j.neubiorev.2022.104559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/10/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.
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Affiliation(s)
- Eva Sheardown
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Aleksandra M Mech
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | | | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Saeedeh Hosseinian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Ian M Sealy
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jose V Torres-Perez
- UK Dementia Research Institute at Imperial College London and Department of Brain Sciences, Imperial College London, 86 Wood Lane, London W12 0BZ, UK
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK.
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9
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Tao D, Zhang H, Yang J, Niu H, Zhang J, Zeng M, Cheng S. PC Splice-Site Variant c.1825+5G>A Caused Intron Retention in a Patient With Pyruvate Carboxylase Deficiency: A Case Report. Front Pediatr 2022; 10:825515. [PMID: 35573952 PMCID: PMC9096210 DOI: 10.3389/fped.2022.825515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/28/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pyruvate carboxylase deficiency (PCD; MIM#266150) is a rare autosomal recessive disorder characterized by a wide range of clinical features, including delayed neurodevelopment, elevated pyruvate levels, lactic acidosis, elevated ketone levels, and hyperammonemia. The pyruvate carboxylase (PC) gene was identified to be the disease-causing gene for PCD. A novel homozygous splice variant in the PC gene was identified in a Chinese boy, but the pathogenicity is still unclear. The objective of the present study was to determine the effect of this splice-site variant by reverse transcription analysis. METHODS We reported the clinical course of a 20-month-old Chinese pediatric patient who was diagnosed with PCD using whole-exome sequencing (WES). The effects of the variant on mRNA splicing were analyzed through the transcript analysis in vivo. RESULTS The results of metabolic blood and urine screening suggested PCD by employing tandem mass spectrometry. WES revealed a novel homozygous splice-site variant (c.1825+5G>A) in the PC gene. in vivo transcript analysis indicated that the splice-site variant caused the retention of 192 bp of the intron. CONCLUSION Thus, c.1825+5G>A was established as a pathogenic variant, thereby enriching the mutational spectrum of the PC gene and providing a basis for the genetic diagnosis of PCD.
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Affiliation(s)
- DongYing Tao
- Department of Pediatrics, XiJing Hospital, Fourth Military Medical University, Xi'an, China
| | - HuiQin Zhang
- Department of Pediatrics, XiJing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - HuanHong Niu
- Department of Pediatrics, XiJing Hospital, Fourth Military Medical University, Xi'an, China
| | - JingJing Zhang
- Department of Pediatrics, XiJing Hospital, Fourth Military Medical University, Xi'an, China
| | - Minghua Zeng
- Medical Experiment and Training Center, Hanzhong Vocational and Technical College, Hanzhong, China
| | - ShengQuan Cheng
- Department of Pediatrics, XiJing Hospital, Fourth Military Medical University, Xi'an, China
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10
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Oluwole OG, Kuivaniemi H, Abrahams S, Haylett WL, Vorster AA, van Heerden CJ, Kenyon CP, Tabb DL, Fawale MB, Sunmonu TA, Ajose A, Olaogun MO, Rossouw AC, van Hillegondsberg LS, Carr J, Ross OA, Komolafe MA, Tromp G, Bardien S. Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson's disease in Black South African and Nigerian patients. BMC MEDICAL GENETICS 2020; 21:23. [PMID: 32019516 PMCID: PMC7001245 DOI: 10.1186/s12881-020-0953-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The prevalence of Parkinson's disease (PD) is increasing in sub-Saharan Africa, but little is known about the genetics of PD in these populations. Due to their unique ancestry and diversity, sub-Saharan African populations have the potential to reveal novel insights into the pathobiology of PD. In this study, we aimed to characterise the genetic variation in known and novel PD genes in a group of Black South African and Nigerian patients. METHODS We recruited 33 Black South African and 14 Nigerian PD patients, and screened them for sequence variants in 751 genes using an Ion AmpliSeq™ Neurological Research panel. We used bcftools to filter variants and annovar software for the annotation. Rare variants were prioritised using MetaLR and MetaSVM prediction scores. The effect of a variant on ATP13A2's protein structure was investigated by molecular modelling. RESULTS We identified 14,655 rare variants with a minor allele frequency ≤ 0.01, which included 2448 missense variants. Notably, no common pathogenic mutations were identified in these patients. Also, none of the known PD-associated mutations were found highlighting the need for more studies in African populations. Altogether, 54 rare variants in 42 genes were considered deleterious and were prioritized, based on MetaLR and MetaSVM scores, for follow-up studies. Protein modelling showed that the S1004R variant in ATP13A2 possibly alters the conformation of the protein. CONCLUSIONS We identified several rare variants predicted to be deleterious in sub-Saharan Africa PD patients; however, further studies are required to determine the biological effects of these variants and their possible role in PD. Studies such as these are important to elucidate the genetic aetiology of this disorder in patients of African ancestry.
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Affiliation(s)
- Oluwafemi G Oluwole
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shameemah Abrahams
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - William L Haylett
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Endocrinology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alvera A Vorster
- DNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Carel J van Heerden
- DNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Colin P Kenyon
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Michael B Fawale
- Neurology Unit, Department of Medicine, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Taofiki A Sunmonu
- Neurology Unit, Department of Medicine, Federal Medical Centre, Owo, Nigeria
| | - Abiodun Ajose
- Department of Chemical Pathology, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Matthew O Olaogun
- Department of Medical Rehabilitation, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Anastasia C Rossouw
- Division of Neurology, Department of Medicine, Faculty of Health Sciences, Walter Sisulu University, East London, South Africa
| | - Ludo S van Hillegondsberg
- Division of Neurology, Department of Medicine, Faculty of Health Sciences, Walter Sisulu University, East London, South Africa
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Clinical Genomics, Mayo Clinic College of Medicine, Jacksonville, Florida, USA
| | - Morenikeji A Komolafe
- Neurology Unit, Department of Medicine, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Cape Town, South Africa.
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa.
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
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11
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Coci EG, Gapsys V, Shur N, Shin‐Podskarbi Y, Groot BL, Miller K, Vockley J, Sondheimer N, Ganetzky R, Freisinger P. Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in
PC
and analysis of the genotype–phenotype correlation. Hum Mutat 2019; 40:816-827. [DOI: 10.1002/humu.23742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Emanuele G. Coci
- Department for NeuropediatricsUniversity Children's Hospital, Ruhr University BochumBochum Germany
- Institute for Neuropediatrics and Social PediatricsHamburg Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics GroupMax Plank Institute for Biophysical ChemistryGöttingen Germany
| | - Natasha Shur
- Division of GeneticsAlbany Medical CenterAlbany New York
- Children's National Medical CenterWashington District of Columbia
| | | | - Bert L. Groot
- Computational Biomolecular Dynamics GroupMax Plank Institute for Biophysical ChemistryGöttingen Germany
| | - Kathryn Miller
- Division of GeneticsAlbany Medical CenterAlbany New York
| | - Jerry Vockley
- Children's Hospital of PittsburghUniversity of Pittsburgh School of MedicinePittsburgh Pennsylvania
| | - Neal Sondheimer
- Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenToronto Ontario Canada
| | - Rebecca Ganetzky
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphia Pennsylvania
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12
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Alves CAPF, Gonçalves FG, Grieb D, Lucato LT, Goldstein AC, Zuccoli G. Neuroimaging of Mitochondrial Cytopathies. Top Magn Reson Imaging 2018; 27:219-240. [PMID: 30086109 DOI: 10.1097/rmr.0000000000000173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mitochondrial diseases are a complex and heterogeneous group of genetic disorders that occur as a result of either nuclear DNA or mitochondrial DNA pathogenic variants, leading to a decrease in oxidative phosphorylation and cellular energy (ATP) production. Increasing knowledge about molecular, biochemical, and genetic abnormalities related to mitochondrial dysfunction has expanded the neuroimaging phenotypes of mitochondrial disorders. As a consequence of this growing field, the imaging recognition patterns of mitochondrial cytopathies are continually evolving. In this review, we describe the main neuroimaging characteristics of pediatric mitochondrial diseases, ranging from classical to more recent and challenging features. Due to the increased knowledge about the imaging findings of mitochondrial cytopathies, the pediatric neuroradiologist plays a crucial role in the diagnosis and evaluation of these patients.
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Affiliation(s)
| | | | - Dominik Grieb
- Department of Radiology and Neuroradiology, Sana Kliniken Duisburg, Germany
| | - Leandro Tavares Lucato
- Neuroradiology Section, Hospital das Clínicas- HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Amy C Goldstein
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA
| | - Giulio Zuccoli
- Department of Radiology, University of Pittsburgh School of Medicine, Director of Pediatric Neuroradiology, Children Hospital of Pittsburgh, Pittsburgh, PA
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13
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Plutino M, Chaussenot A, Rouzier C, Ait-El-Mkadem S, Fragaki K, Paquis-Flucklinger V, Bannwarth S. Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases. BMC MEDICAL GENETICS 2018; 19:57. [PMID: 29625556 PMCID: PMC5889585 DOI: 10.1186/s12881-018-0568-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 12/29/2022]
Abstract
Background Since the advent of next generation sequencing (NGS), several studies have tried to evaluate the relevance of targeted gene panel sequencing and whole exome sequencing for molecular diagnosis of mitochondrial diseases. The comparison between these different strategies is extremely difficult. A recent study analysed a cohort of patients affected by a mitochondrial disease using a NGS approach based on a targeted gene panel including 132 genes. This strategy led to identify the causative mutations in 15.2% of cases. The number of novel genes responsible for respiratory chain deficiency increases very rapidly. Methods In order to determine the impact of larger panels used as a first screening strategy on molecular diagnosis success, we analysed a cohort of 80 patients affected by a mitochondrial disease with a first mitochondrial DNA (mtDNA) NGS screening and secondarily a targeted mitochondrial panel of 281 nuclear genes. Results Pathogenic mtDNA abnormalities were identified in 4.1% (1/24) of children and 25% (14/56) of adult patients. The remaining 65 patients were analysed with our targeted mitochondrial panel and this approach enabled us to achieve an identification rate of 21.7% (5/23) in children versus 7.1% (3/42) in adults. Conclusions Our results confirm that larger gene panels do not improve diagnostic yield of mitochondrial diseases due to (i) their very high genetic heterogeneity, (ii) the ongoing discovery of novel genes and (iii) mutations in genes apparently not related to mitochondrial function that lead to secondary respiratory chain deficiency. Electronic supplementary material The online version of this article (10.1186/s12881-018-0568-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morgane Plutino
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France
| | | | - Cécile Rouzier
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France
| | | | | | | | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France. .,IRCAN UMR CNRS 7284/INSERM U1081, Medicine School, 28 av de Valombrose, 06107, Nice cedex 2, France.
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14
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Abstract
Pyruvate carboxylase is a metabolic enzyme that fuels the tricarboxylic acid cycle with one of its intermediates and also participates in the first step of gluconeogenesis. This large enzyme is multifunctional, and each subunit contains two active sites that catalyze two consecutive reactions that lead to the carboxylation of pyruvate into oxaloacetate, and a binding site for acetyl-CoA, an allosteric regulator of the enzyme. Pyruvate carboxylase oligomers arrange in tetramers and covalently attached biotins mediate the transfer of carboxyl groups between distant active sites. In this chapter, some of the recent findings on pyruvate carboxylase functioning are presented, with special focus on the structural studies of the full length enzyme. The emerging picture reveals large movements of domains that even change the overall quaternary organization of pyruvate carboxylase tetramers during catalysis.
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Affiliation(s)
- Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160, Derio, Spain.
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15
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Legati A, Reyes A, Nasca A, Invernizzi F, Lamantea E, Tiranti V, Garavaglia B, Lamperti C, Ardissone A, Moroni I, Robinson A, Ghezzi D, Zeviani M. New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1326-1335. [PMID: 26968897 DOI: 10.1016/j.bbabio.2016.02.022] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/17/2016] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Next Generation Sequencing (NGS) technologies are revolutionizing the diagnostic screening for rare disease entities, including primary mitochondrial disorders, particularly those caused by nuclear gene defects. NGS approaches are able to identify the causative gene defects in small families and even single individuals, unsuitable for investigation by traditional linkage analysis. These technologies are contributing to fill the gap between mitochondrial disease cases defined on the basis of clinical, neuroimaging and biochemical readouts, which still outnumber by approximately 50% the cases for which a molecular-genetic diagnosis is attained. We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. Not only this approach has allowed us to reach molecular diagnosis in a significant fraction (20%) of these difficult cases, but it has also revealed unexpected and conceptually new findings. These include the possibility of marked variable penetrance of recessive mutations, the identification of large-scale DNA rearrangements, which explain spuriously heterozygous cases, and the association of mutations in known genes with unusual, previously unreported clinical phenotypes. Importantly, WES on selected cases has unraveled the presence of pathogenic mutations in genes encoding non-mitochondrial proteins (e.g. the transcription factor E4F1), an observation that further expands the intricate genetics of mitochondrial disease and suggests a new area of investigation in mitochondrial medicine. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Andrea Legati
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Aurelio Reyes
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK
| | - Alessia Nasca
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Federica Invernizzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Eleonora Lamantea
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Barbara Garavaglia
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Costanza Lamperti
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Anna Ardissone
- Unit of Child Neurology, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Isabella Moroni
- Unit of Child Neurology, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Alan Robinson
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK
| | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy.
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK.
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16
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Wolman MA, Jain RA, Marsden KC, Bell H, Skinner J, Hayer KE, Hogenesch JB, Granato M. A genome-wide screen identifies PAPP-AA-mediated IGFR signaling as a novel regulator of habituation learning. Neuron 2015; 85:1200-11. [PMID: 25754827 DOI: 10.1016/j.neuron.2015.02.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/06/2015] [Accepted: 02/12/2015] [Indexed: 01/15/2023]
Abstract
Habituation represents a fundamental form of learning, yet the underlying molecular genetic mechanisms are not well defined. Here we report on a genome-wide genetic screen, coupled with whole-genome sequencing, that identified 14 zebrafish startle habituation mutants including mutants of the vertebrate-specific gene pregnancy-associated plasma protein-aa (pappaa). PAPP-AA encodes an extracellular metalloprotease known to increase IGF bioavailability, thereby enhancing IGF receptor signaling. We find that pappaa is expressed by startle circuit neurons, and expression of wild-type but not a metalloprotease-inactive version of pappaa restores habituation in pappaa mutants. Furthermore, acutely inhibiting IGF1R function in wild-type reduces habituation, while activation of IGF1R downstream effectors in pappaa mutants restores habituation, demonstrating that pappaa promotes learning by acutely and locally increasing IGF bioavailability. In sum, our results define the first functional gene set for habituation learning in a vertebrate and identify PAPPAA-regulated IGF signaling as a novel mechanism regulating habituation learning.
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Affiliation(s)
- Marc A Wolman
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA; Department of Zoology, University of Wisconsin; 213 Zoology Research Building, 1117 West Johnson Street, Madison, WI 53706, USA
| | - Roshan A Jain
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Kurt C Marsden
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Hannah Bell
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Julianne Skinner
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Katharina E Hayer
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 829 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 829 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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17
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Habarou F, Brassier A, Rio M, Chrétien D, Monnot S, Barbier V, Barouki R, Bonnefont JP, Boddaert N, Chadefaux-Vekemans B, Le Moyec L, Bastin J, Ottolenghi C, de Lonlay P. Pyruvate carboxylase deficiency: An underestimated cause of lactic acidosis. Mol Genet Metab Rep 2014. [PMID: 28649521 PMCID: PMC5471145 DOI: 10.1016/j.ymgmr.2014.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pyruvate carboxylase (PC) is a biotin-containing mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate, thereby being involved in gluconeogenesis and in energy production through replenishment of the tricarboxylic acid (TCA) cycle with oxaloacetate. PC deficiency is a very rare metabolic disorder. We report on a new patient affected by the moderate form (the American type A). Diagnosis was nearly fortuitous, resulting from the revision of an initial diagnosis of mitochondrial complex IV (C IV) defect. The patient presented with severe lactic acidosis and pronounced ketonuria, associated with lethargy at age 23 months. Intellectual disability was noted at this time. Amino acids in plasma and organic acids in urine did not show patterns of interest for the diagnostic work-up. In skin fibroblasts PC showed no detectable activity whereas biotinidase activity was normal. We had previously reported another patient with the severe form of PC deficiency and we show that she also had secondary C IV deficiency in fibroblasts. Different anaplerotic treatments in vivo and in vitro were tested using fibroblasts of both patients with 2 different types of PC deficiency, type A (patient 1) and type B (patient 2). Neither clinical nor biological effects in vivo and in vitro were observed using citrate, aspartate, oxoglutarate and bezafibrate. In conclusion, this case report suggests that the moderate form of PC deficiency may be underdiagnosed and illustrates the challenges raised by energetic disorders in terms of diagnostic work-up and therapeutical strategy even in a moderate form.
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Affiliation(s)
- F Habarou
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,INSERM U1124, Université Paris Descartes, Paris, France.,Service de Biochimie Métabolomique et Protéomique, Hôpital Necker, APHP, Paris, France
| | - A Brassier
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,Université Paris Descartes, Paris, France
| | - M Rio
- Département de Génétique, Hôpital Necker, APHP, Paris, France
| | | | - S Monnot
- Département de Génétique, Hôpital Necker, APHP, Paris, France.,IHU Imagine, UMR1163, France
| | - V Barbier
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France
| | - R Barouki
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,INSERM U1124, Université Paris Descartes, Paris, France.,Service de Biochimie Métabolomique et Protéomique, Hôpital Necker, APHP, Paris, France
| | - J P Bonnefont
- Département de Génétique, Hôpital Necker, APHP, Paris, France.,INSERM U781, Paris, France
| | - N Boddaert
- Service de Radiologie Pédiatrique, Hôpital Necker, APHP, Paris, France
| | - B Chadefaux-Vekemans
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,INSERM U1124, Université Paris Descartes, Paris, France.,Service de Biochimie Métabolomique et Protéomique, Hôpital Necker, APHP, Paris, France
| | - L Le Moyec
- INSERM U902, Université d'Evry Val d'Essonne, INSERM UBIAE U902, Boulevard François Miterrand, 91025 Evry, France
| | - J Bastin
- INSERM U1124, Université Paris Descartes, Paris, France
| | - C Ottolenghi
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,INSERM U1124, Université Paris Descartes, Paris, France.,Service de Biochimie Métabolomique et Protéomique, Hôpital Necker, APHP, Paris, France
| | - P de Lonlay
- Centre de Référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, APHP, Paris, France.,Université Paris Descartes, Paris, France.,INSERM U781, Paris, France
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18
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Sheng X, Liu Y. QM/MM Study of the Reaction Mechanism of the Carboxyl Transferase Domain of Pyruvate Carboxylase from Staphylococcus aureus. Biochemistry 2014; 53:4455-66. [DOI: 10.1021/bi500020r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiang Sheng
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
- Northwest
Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
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19
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Lietzan AD, St. Maurice M. Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity. Arch Biochem Biophys 2014; 544:75-86. [DOI: 10.1016/j.abb.2013.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 12/31/2022]
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20
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Abstract
Pyruvate dehydrogenase and pyruvate carboxylase deficiency are the most common disorders in pyruvate metabolism. Diagnosis is made by enzymatic and DNA analysis after basic biochemical tests in plasma, urine, and CSF. Pyruvate dehydrogenase has three main subunits, an additional E3-binding protein and two complex regulatory enzymes. Most frequent are deficiencies in PDH-E1α. There is a spectrum of clinical presentations in E1α deficiency, ranging in boys from severe neonatal lactic acidosis, Leigh encephalopathy, to later onset of neurological disease such as intermittent ataxia or dystonia. Females tend to have a more uniform presentation resembling nonprogressive cerebral palsy. Neuroradiological abnormalities such as corpus callosum agenesis are seen more frequently in girls, basal ganglia and midbrain disturbances in boys. Deficiencies in the other subunits have also been described, but in a smaller number of patients. Pyruvate carboxylase deficiency has three clinical phenotypes. The infantile type is characterized mainly by severe developmental delay, failure to thrive, and seizures. The second type is characterized by neonatal onset of severe lactic acidosis with rigidity and hypokinesia. A third form is rarer with intermittent episodes of lactic acidosis and ketoacidosis. Neuroradiological findings such as cystic periventricular leukomalacia have been described.
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21
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Abstract
We have investigated seven patients with the type B form of pyruvate carboxylase (PC) deficiency. Mutation analysis revealed eight mutations, all novel. In a patient with exon skipping on cDNA analysis, we identified a homozygous mutation located in a potential branch point sequence, the first possible branch point mutation in PC. Two patients were homozygous for missense mutations (with normal protein amounts on western blot analysis), and two patients were homozygous for nonsense mutations. In addition, a duplication of one base pair was found in a patient who also harboured a splice site mutation. Another splice site mutation led to the activation of a cryptic splice site, shown by cDNA analysis.All patients reported until now with at least one missense mutation have had the milder type A form of PC deficiency. We thus report for the first time two patients with homozygous missense mutations with the severe type B deficiency, clinically indistinguishable from other patients with type B form of PC deficiency.The mutations found here are novel; it is noteworthy that four Turkish patients did not have any mutations in common, despite the rarity of PC deficiency. There is thus no evidence for recurrent mutations in the Turkish or other populations.
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22
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Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012; 70:863-91. [PMID: 22869039 DOI: 10.1007/s00018-012-1096-0] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 12/14/2022]
Abstract
Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase, pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT), and biotin-carboxyl carrier protein components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC, or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC, and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.
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23
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Lietzan AD, Menefee AL, Zeczycki TN, Kumar S, Attwood PV, Wallace JC, Cleland WW, St Maurice M. Interaction between the biotin carboxyl carrier domain and the biotin carboxylase domain in pyruvate carboxylase from Rhizobium etli. Biochemistry 2011; 50:9708-23. [PMID: 21958016 DOI: 10.1021/bi201277j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family.
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Affiliation(s)
- Adam D Lietzan
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, United States
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Marin-Valencia I, Roe CR, Pascual JM. Pyruvate carboxylase deficiency: mechanisms, mimics and anaplerosis. Mol Genet Metab 2010; 101:9-17. [PMID: 20598931 DOI: 10.1016/j.ymgme.2010.05.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 05/26/2010] [Indexed: 11/30/2022]
Abstract
Pyruvate carboxylase (PC) is a regulated mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate, a critical transition that replenishes citric acid cycle intermediates and facilitates other biosynthetic reactions that drive anabolism. Its deficiency causes multiorgan metabolic imbalance that predominantly manifests with lactic acidemia and neurological dysfunction at an early age. Three clinical forms of PC deficiency have been identified: an infantile form (Type A), a severe neonatal form (Type B), and a benign form (Type C), all of which exhibit clinical or biochemical correlates of impaired anaplerosis. There is no effective treatment for these patients and most, except those affected by the benign form, die in early life. We review the physiology of this enzyme and dissect the major clinical, biochemical, and genetic aspects of its dysfunction, emphasizing features that distinguish PC deficiency from other causes of lactic acidemia that render PC deficiency potentially treatable using novel interventions capable of enhancing anaplerosis.
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Affiliation(s)
- Isaac Marin-Valencia
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX 75390-8813, USA
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