1
|
van Karnebeek CDM, Tarailo-Graovac M, Leen R, Meinsma R, Correard S, Jansen-Meijer J, Prykhozhij SV, Pena IA, Ban K, Schock S, Saxena V, Pras-Raves ML, Drögemöller BI, Grootemaat AE, van der Wel NN, Dobritzsch D, Roseboom W, Schomakers BV, Jaspers YRJ, Zoetekouw L, Roelofsen J, Ferreira CR, van der Lee R, Ross CJ, Kochan J, McIntyre RL, van Klinken JB, van Weeghel M, Kramer G, Weschke B, Labrune P, Willemsen MA, Riva D, Garavaglia B, Moeschler JB, Filiano JJ, Ekker M, Berman JN, Dyment D, Vaz FM, Wassermann WW, Houtkooper RH, van Kuilenburg ABP. CIAO1 and MMS19 deficiency: A lethal neurodegenerative phenotype caused by cytosolic Fe-S cluster protein assembly disorders. Genet Med 2024; 26:101104. [PMID: 38411040 DOI: 10.1016/j.gim.2024.101104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024] Open
Abstract
PURPOSE The functionality of many cellular proteins depends on cofactors; yet, they have only been implicated in a minority of Mendelian diseases. Here, we describe the first 2 inherited disorders of the cytosolic iron-sulfur protein assembly system. METHODS Genetic testing via genome sequencing was applied to identify the underlying disease cause in 3 patients with microcephaly, congenital brain malformations, progressive developmental and neurologic impairments, recurrent infections, and a fatal outcome. Studies in patient-derived skin fibroblasts and zebrafish models were performed to investigate the biochemical and cellular consequences. RESULTS Metabolic analysis showed elevated uracil and thymine levels in body fluids but no pathogenic variants in DPYD, encoding dihydropyrimidine dehydrogenase. Genome sequencing identified compound heterozygosity in 2 patients for missense variants in CIAO1, encoding cytosolic iron-sulfur assembly component 1, and homozygosity for an in-frame 3-nucleotide deletion in MMS19, encoding the MMS19 homolog, cytosolic iron-sulfur assembly component, in the third patient. Profound alterations in the proteome, metabolome, and lipidome were observed in patient-derived fibroblasts. We confirmed the detrimental effect of deficiencies in CIAO1 and MMS19 in zebrafish models. CONCLUSION A general failure of cytosolic and nuclear iron-sulfur protein maturation caused pleiotropic effects. The critical function of the cytosolic iron-sulfur protein assembly machinery for antiviral host defense may well explain the recurrent severe infections occurring in our patients.
Collapse
Affiliation(s)
- Clara D M van Karnebeek
- Amsterdam UMC location University of Amsterdam, Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; United for Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Maja Tarailo-Graovac
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute (ACHRI), Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - René Leen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Rutger Meinsma
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Solenne Correard
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Judith Jansen-Meijer
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Sergey V Prykhozhij
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Izabella A Pena
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology-MIT, Boston, MA
| | - Kevin Ban
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Schock
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Vishal Saxena
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Mia L Pras-Raves
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Britt I Drögemöller
- Rady Faculty of Health Sciences, Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anita E Grootemaat
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Doreen Dobritzsch
- Uppsala University, Department of Chemistry, Biomedical Center, Uppsala, Sweden
| | - Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bauke V Schomakers
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Yorrick R J Jaspers
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Lida Zoetekouw
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jeroen Roelofsen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Robin van der Lee
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Jakub Kochan
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biochemistry, Kraków, Poland
| | - Rebecca L McIntyre
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jan B van Klinken
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel van Weeghel
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gertjan Kramer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, Berlin, Germany
| | - Philippe Labrune
- APHP-Université Paris-Saclay, Hôpital Antoine Béclère, Centre de Référence Maladies Héréditaires du Métabolisme Hépatique, Service de Pédiatrie, Clamart, and Paris-Saclay University, and INSERM U 1195, Clamart, France
| | - Michèl A Willemsen
- Department of Pediatric Neurology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daria Riva
- Neurogenetic Syndromes and Autism Spectrum Disorders Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - Barbara Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - John B Moeschler
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - James J Filiano
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jason N Berman
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - David Dyment
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Frédéric M Vaz
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wyeth W Wassermann
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Riekelt H Houtkooper
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - André B P van Kuilenburg
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands.
| |
Collapse
|
2
|
Jia JJ, Lahr RM, Solgaard MT, Moraes BJ, Pointet R, Yang AD, Celucci G, Graber TE, Hoang HD, Niklaus M, Pena IA, Hollensen AK, Smith EM, Chaker-Margot M, Anton L, Dajadian C, Livingstone M, Hearnden J, Wang XD, Yu Y, Maier T, Damgaard CK, Berman AJ, Alain T, Fonseca BD. mTORC1 promotes TOP mRNA translation through site-specific phosphorylation of LARP1. Nucleic Acids Res 2021; 49:3461-3489. [PMID: 33398329 PMCID: PMC8034618 DOI: 10.1093/nar/gkaa1239] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 11/29/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
LARP1 is a key repressor of TOP mRNA translation. It binds the m7Gppp cap moiety and the adjacent 5'TOP motif of TOP mRNAs, thus impeding the assembly of the eIF4F complex on these transcripts. mTORC1 controls TOP mRNA translation via LARP1, but the details of the mechanism are unclear. Herein we elucidate the mechanism by which mTORC1 controls LARP1's translation repression activity. We demonstrate that mTORC1 phosphorylates LARP1 in vitro and in vivo, activities that are efficiently inhibited by rapamycin and torin1. We uncover 26 rapamycin-sensitive phospho-serine and -threonine residues on LARP1 that are distributed in 7 clusters. Our data show that phosphorylation of a cluster of residues located proximally to the m7Gppp cap-binding DM15 region is particularly sensitive to rapamycin and regulates both the RNA-binding and the translation inhibitory activities of LARP1. Our results unravel a new model of translation control in which the La module (LaMod) and DM15 region of LARP1, both of which can directly interact with TOP mRNA, are differentially regulated: the LaMod remains constitutively bound to PABP (irrespective of the activation status of mTORC1), while the C-terminal DM15 'pendular hook' engages the TOP mRNA 5'-end to repress translation, but only in conditions of mTORC1 inhibition.
Collapse
Affiliation(s)
- Jian-Jun Jia
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Roni M Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael T Solgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bruno J Moraes
- GABBA PhD Program, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
- PrimerGen Ltd, Viseu, Portugal
| | - Roberta Pointet
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - An-Dao Yang
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Giovanna Celucci
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Marius R Niklaus
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Anne K Hollensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ewan M Smith
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Leonie Anton
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christopher Dajadian
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Mark Livingstone
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Jaclyn Hearnden
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Canada
| | - Xu-Dong Wang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yonghao Yu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christian K Damgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tommy Alain
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - Bruno D Fonseca
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- PrimerGen Ltd, Viseu, Portugal
| |
Collapse
|
3
|
Kory N, Uit de Bos J, van der Rijt S, Jankovic N, Güra M, Arp N, Pena IA, Prakash G, Chan SH, Kunchok T, Lewis CA, Sabatini DM. MCART1/SLC25A51 is required for mitochondrial NAD transport. Sci Adv 2020; 6:sciadv.abe5310. [PMID: 33087354 PMCID: PMC7577609 DOI: 10.1126/sciadv.abe5310] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 05/19/2023]
Abstract
The nicotinamide adenine dinucleotide (NAD+/NADH) pair is a cofactor in redox reactions and is particularly critical in mitochondria as it connects substrate oxidation by the tricarboxylic acid (TCA) cycle to adenosine triphosphate generation by the electron transport chain (ETC) and oxidative phosphorylation. While a mitochondrial NAD+ transporter has been identified in yeast, how NAD enters mitochondria in metazoans is unknown. Here, we mine gene essentiality data from human cell lines to identify MCART1 (SLC25A51) as coessential with ETC components. MCART1-null cells have large decreases in TCA cycle flux, mitochondrial respiration, ETC complex I activity, and mitochondrial levels of NAD+ and NADH. Isolated mitochondria from cells lacking or overexpressing MCART1 have greatly decreased or increased NAD uptake in vitro, respectively. Moreover, MCART1 and NDT1, a yeast mitochondrial NAD+ transporter, can functionally complement for each other. Thus, we propose that MCART1 is the long sought mitochondrial transporter for NAD in human cells.
Collapse
Affiliation(s)
- Nora Kory
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Jelmi Uit de Bos
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Sanne van der Rijt
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Nevena Jankovic
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Miriam Güra
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Nicholas Arp
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Izabella A Pena
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Gyan Prakash
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| |
Collapse
|
4
|
Gillespie MK, McMillan HJ, Kernohan KD, Pena IA, Meyer-Schuman R, Antonellis A, Boycott KM. A Novel Mutation in MARS in a Patient with Charcot-Marie-Tooth Disease, Axonal, Type 2U with Congenital Onset. J Neuromuscul Dis 2020; 6:333-339. [PMID: 31356216 PMCID: PMC6889022 DOI: 10.3233/jnd-190404] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Charcot-Marie-Tooth disease is a phenotypically and genetically heterogeneous group of disorders affecting both motor and sensory neurons. Exome sequencing has driven discovery of genes responsible for Charcot-Marie-Tooth disease with more than 70 genes now associated with this neuromuscular disease. The MARS gene was recently reported as the cause of Charcot-Marie-Tooth 2U, a slowly progressive axonal sensorimotor polyneuropathy with adult-onset reported in six patients. We report here a patient with a progressive, early childhood-onset, motor-predominant form of Charcot-Marie-Tooth disease. Exome sequencing identified a novel MARS variant (c.1189G>A; p.Ala397Thr) that was not present in her unaffected mother; her unaffected father was unavailable. Further studies using structural modeling and a yeast humanization assay support pathogenicity of the variant. Our study expands the phenotype of Charcot-Marie-Tooth 2U, while highlighting the utility of functional assays to evaluate variant pathogenicity.
Collapse
Affiliation(s)
- Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Hugh J McMillan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | | | | | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| |
Collapse
|
5
|
Boycott KM, Campeau PM, Howley HE, Pavlidis P, Rogic S, Oriel C, Berman JN, Hamilton RM, Hicks GG, Lipshitz HD, Masson JY, Shoubridge EA, Junker A, Leroux MR, McMaster CR, Michaud JL, Turvey SE, Dyment D, Innes AM, van Karnebeek CD, Lehman A, Cohn RD, MacDonald IM, Rachubinski RA, Frosk P, Vandersteen A, Wozniak RW, Pena IA, Wen XY, Lacaze-Masmonteil T, Rankin C, Hieter P. The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms. Am J Hum Genet 2020; 106:143-152. [PMID: 32032513 DOI: 10.1016/j.ajhg.2020.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have transformed our ability to identify the genetic causes of rare diseases (RDs), yet we have a limited understanding of the mechanistic roles of most genes in health and disease. When a novel RD gene is first discovered, there is minimal insight into its biological function, the pathogenic mechanisms of disease-causing variants, and how therapy might be approached. To address this gap, the Canadian Rare Diseases Models and Mechanisms (RDMM) Network was established to connect clinicians discovering new disease genes with Canadian scientists able to study equivalent genes and pathways in model organisms (MOs). The Network is built around a registry of more than 500 Canadian MO scientists, representing expertise for over 7,500 human genes. RDMM uses a committee process to identify and evaluate clinician-MO scientist collaborations and approve 25,000 Canadian dollars in catalyst funding. To date, we have made 85 clinician-MO scientist connections and funded 105 projects. These collaborations help confirm variant pathogenicity and unravel the molecular mechanisms of RD, and also test novel therapies and lead to long-term collaborations. To expand the impact and reach of this model, we made the RDMM Registry open-source, portable, and customizable, and we freely share our committee structures and processes. We are currently working with emerging networks in Europe, Australia, and Japan to link international RDMM networks and registries and enable matches across borders. We will continue to create meaningful collaborations, generate knowledge, and advance RD research locally and globally for the benefit of patients and families living with RD.
Collapse
Affiliation(s)
- Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Philippe M Campeau
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Heather E Howley
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christine Oriel
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada
| | - Jason N Berman
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Robert M Hamilton
- Labatt Family Heart Centre and Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Geoffrey G Hicks
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Eric A Shoubridge
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Anne Junker
- Department of Pediatrics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Jaques L Michaud
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Stuart E Turvey
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - David Dyment
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital, Calgary, AB T2N 4N1, Canada
| | - Clara D van Karnebeek
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pediatrics, Amsterdam University Medical Centres, Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - Richard A Rachubinski
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Patrick Frosk
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Anthony Vandersteen
- Department of Pediatrics, Maritime Medical Genetics Service, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Richard W Wozniak
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Izabella A Pena
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, St Michael's Hospital, Unity Health Toronto, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8
| | - Thierry Lacaze-Masmonteil
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Catharine Rankin
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
6
|
Johnstone DL, Al-Shekaili HH, Tarailo-Graovac M, Wolf NI, Ivy AS, Demarest S, Roussel Y, Ciapaite J, van Roermund CWT, Kernohan KD, Kosuta C, Ban K, Ito Y, McBride S, Al-Thihli K, Abdelrahim RA, Koul R, Al Futaisi A, Haaxma CA, Olson H, Sigurdardottir LY, Arnold GL, Gerkes EH, Boon M, Heiner-Fokkema MR, Noble S, Bosma M, Jans J, Koolen DA, Kamsteeg EJ, Drögemöller B, Ross CJ, Majewski J, Cho MT, Begtrup A, Wasserman WW, Bui T, Brimble E, Violante S, Houten SM, Wevers RA, van Faassen M, Kema IP, Lepage N, Lines MA, Dyment DA, Wanders RJA, Verhoeven-Duif N, Ekker M, Boycott KM, Friedman JM, Pena IA, van Karnebeek CDM. PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights. Brain 2020; 142:542-559. [PMID: 30668673 DOI: 10.1093/brain/awy346] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/30/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.
Collapse
Affiliation(s)
- Devon L Johnstone
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Hilal H Al-Shekaili
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Maja Tarailo-Graovac
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Institute of Physiology and Biochemistry, Faculty of Biology, The University of Belgrade, Belgrade, Serbia.,Departments of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam University Medical Centres, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Autumn S Ivy
- Division of Child Neurology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, CA, USA
| | - Scott Demarest
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Children's Hospital Colorado, CO, USA
| | - Yann Roussel
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jolita Ciapaite
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Carlo W T van Roermund
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Ceres Kosuta
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kevin Ban
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Skye McBride
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Khalid Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Rana A Abdelrahim
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Roshan Koul
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al Futaisi
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute of Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Heather Olson
- Department of Neurology, Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, MA, USA
| | - Laufey Yr Sigurdardottir
- Department of Neurology, University of Central Florida, Nemours Children's Hospital, Orlando, FL, USA
| | - Georgianne L Arnold
- Department of Pediatrics, University of Pittsburgh Medical Center, Pittsburg, PA, USA
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Boon
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandra Noble
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Marjolein Bosma
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Judith Jans
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Britt Drögemöller
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | | | - Wyeth W Wasserman
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tuan Bui
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron A Wevers
- United for Metabolic Diseases, The Netherlands.,Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nathalie Lepage
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Matthew A Lines
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Ronald J A Wanders
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Nanda Verhoeven-Duif
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Clara D M van Karnebeek
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,United for Metabolic Diseases, The Netherlands.,Departments of Pediatrics and Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,Centre for Molecular Medicine and Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
7
|
Riché R, Liao M, Pena IA, Leung KY, Lepage N, Greene NDE, Sarafoglou K, Schimmenti LA, Drapeau P, Samarut É. Glycine decarboxylase deficiency-induced motor dysfunction in zebrafish is rescued by counterbalancing glycine synaptic level. JCI Insight 2018; 3:124642. [PMID: 30385710 DOI: 10.1172/jci.insight.124642] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 11/17/2022] Open
Abstract
Glycine encephalopathy (GE), or nonketotic hyperglycinemia (NKH), is a rare recessive genetic disease caused by defective glycine cleavage and characterized by increased accumulation of glycine in all tissues. Here, based on new case reports of GLDC loss-of-function mutations in GE patients, we aimed to generate a zebrafish model of severe GE in order to unravel the molecular mechanism of the disease. Using CRISPR/Cas9, we knocked out the gldc gene and showed that gldc-/- fish recapitulate GE on a molecular level and present a motor phenotype reminiscent of severe GE symptoms. The molecular characterization of gldc-/- mutants showed a broad metabolic disturbance affecting amino acids and neurotransmitters other than glycine, with lactic acidosis at stages preceding death. Although a transient imbalance was found in cell proliferation in the brain of gldc-/- zebrafish, the main brain networks were not affected, thus suggesting that GE pathogenicity is mainly due to metabolic defects. We confirmed that the gldc-/- hypotonic phenotype is due to NMDA and glycine receptor overactivation, and demonstrated that gldc-/- larvae depict exacerbated hyperglycinemia at these synapses. Remarkably, we were able to rescue the motor dysfunction of gldc-/- larvae by counterbalancing pharmacologically or genetically the level of glycine at the synapse.
Collapse
Affiliation(s)
- Raphaëlle Riché
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada
| | - Meijiang Liao
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute and Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - Kit-Yi Leung
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nathalie Lepage
- Children's Hospital of Eastern Ontario Research Institute and Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - Nicolas DE Greene
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Kyriakie Sarafoglou
- Division of Pediatric Endocrinology, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Otorhinolaryngology.,Department of Pediatrics, and.,Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Pierre Drapeau
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada.,DanioDesign Inc., Montréal, Quebec, Canada
| | - Éric Samarut
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada.,DanioDesign Inc., Montréal, Quebec, Canada
| |
Collapse
|
8
|
Ito YA, Smith AC, Kernohan KD, Pena IA, Ahmed A, McDonell LM, Beaulieu C, Bulman DE, Smidt A, Sawyer SL, Dyment DA, Boycott KM, Clericuzio CL. A ZPR1 mutation is associated with a novel syndrome of growth restriction, distinct craniofacial features, alopecia, and hypoplastic kidneys. Clin Genet 2018; 94:303-312. [PMID: 29851065 DOI: 10.1111/cge.13388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 12/24/2022]
Abstract
A novel autosomal recessive disorder characterized by pre- and postnatal growth restriction with microcephaly, distinctive craniofacial features, congenital alopecia, hypoplastic kidneys with renal insufficiency, global developmental delay, severe congenital sensorineural hearing loss, early mortality, hydrocephalus, and genital hypoplasia was observed in 4 children from 3 families of New Mexican Hispanic heritage. Three of the children died before 3 years of age from uremia and/or sepsis. Exome sequencing of the surviving individual identified a homozygous c.587T>C (p.Ile196Thr) mutation in ZPR1 Zinc Finger (ZPR1) that segregated appropriately in her family. In a second family, the identical variant was shown to be heterozygous in the affected individual's parents and not homozygous in any of her unaffected siblings. ZPR1 is a ubiquitously expressed, highly conserved protein postulated to transmit proliferative signals from the cell membrane to the nucleus. Structural modeling reveals that p.Ile196Thr disrupts the hydrophobic core of ZPR1. Patient fibroblast cells showed no detectable levels of ZPR1 and the cells showed a defect in cell cycle progression where a significant number of cells remained arrested in the G1 phase. We provide genetic and molecular evidence that a homozygous missense mutation in ZPR1 is associated with a rare and recognizable multisystem syndrome.
Collapse
Affiliation(s)
- Y A Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A C Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - K D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - I A Pena
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A Ahmed
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L M McDonell
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A Smidt
- Division of Genetics/Dysmorphology, Department of Pediatrics, University of New Mexico School of Medicine, Albuquerque, New Mexico.,Department of Dermatology, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Clericuzio
- Division of Genetics/Dysmorphology, Department of Pediatrics, University of New Mexico School of Medicine, Albuquerque, New Mexico
| |
Collapse
|
9
|
Pena IA, Roussel Y, Daniel K, Mongeon K, Johnstone D, Weinschutz Mendes H, Bosma M, Saxena V, Lepage N, Chakraborty P, Dyment DA, van Karnebeek CDM, Verhoeven-Duif N, Bui TV, Boycott KM, Ekker M, MacKenzie A. Pyridoxine-Dependent Epilepsy in Zebrafish Caused by Aldh7a1 Deficiency. Genetics 2017; 207:1501-1518. [PMID: 29061647 PMCID: PMC5714462 DOI: 10.1534/genetics.117.300137] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/04/2017] [Indexed: 11/25/2022] Open
Abstract
Pyridoxine-dependent epilepsy (PDE) is a rare disease characterized by mutations in the lysine degradation gene ALDH7A1 leading to recurrent neonatal seizures, which are uniquely alleviated by high doses of pyridoxine or pyridoxal 5'-phosphate (vitamin B6 vitamers). Despite treatment, neurodevelopmental disabilities are still observed in most PDE patients underlining the need for adjunct therapies. Over 60 years after the initial description of PDE, we report the first animal model for this disease: an aldh7a1-null zebrafish (Danio rerio) displaying deficient lysine metabolism and spontaneous and recurrent seizures in the larval stage (10 days postfertilization). Epileptiform electrographic activity was observed uniquely in mutants as a series of population bursts in tectal recordings. Remarkably, as is the case in human PDE, the seizures show an almost immediate sensitivity to pyridoxine and pyridoxal 5'-phosphate, with a resulting extension of the life span. Lysine supplementation aggravates the phenotype, inducing earlier seizure onset and death. By using mass spectrometry techniques, we further explored the metabolic effect of aldh7a1 knockout. Impaired lysine degradation with accumulation of PDE biomarkers, B6 deficiency, and low γ-aminobutyric acid levels were observed in the aldh7a1-/- larvae, which may play a significant role in the seizure phenotype and PDE pathogenesis. This novel model provides valuable insights into PDE pathophysiology; further research may offer new opportunities for drug discovery to control seizure activity and improve neurodevelopmental outcomes for PDE.
Collapse
Affiliation(s)
- Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Yann Roussel
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Kate Daniel
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - Kevin Mongeon
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
| | - Devon Johnstone
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
| | | | - Marjolein Bosma
- Departments of Pediatrics and Clinical Genetics, Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Vishal Saxena
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Nathalie Lepage
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
| | - Clara D M van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
| | - Nanda Verhoeven-Duif
- Department of Genetics, Center for Molecular Medicine, University Medical Center (UMC), 3584 EA Utrecht, The Netherlands
| | - Tuan Vu Bui
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Alex MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ontario K1H 8L1, Canada
| |
Collapse
|
10
|
Pena IA, Marques LA, Laranjeira ABA, Yunes JA, Eberlin MN, Arruda P. Simultaneous detection of lysine metabolites by a single LC-MS/MS method: monitoring lysine degradation in mouse plasma. Springerplus 2016; 5:172. [PMID: 27026869 PMCID: PMC4766172 DOI: 10.1186/s40064-016-1809-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/12/2016] [Indexed: 11/16/2022]
Abstract
Detection and quantification of lysine degradation metabolites in plasma is necessary for the diagnosis and follow-up of diseases such as pyridoxine-dependent epilepsy. The principal metabolites involved in the disease are related to the first steps of lysine oxidation, either through the saccharopine or the pipecolate pathways. Currently, there are three different analytical methods used to assess the content of these metabolites in urine and plasma, but they require different sample preparations and analytical equipment. Here, we describe a protocol that calls for a simple sample preparation and uses liquid chromatography tandem mass spectrometry (LC–MS/MS) that allows simultaneous detection and quantification of underivatized l-saccharopine, l-aminoadipic acid, l-pipecolic acid, piperideine-6-carboxylate, l-glutamic acid, and pyridoxal-5-phosphate in plasma samples. To validate the method we analyzed the time course degradation after intraperitoneal injection of l-lysine in C57BL/6/J mice. We observed that the degradation of lysine through the saccharopine pathway reached a maximum within the first 2 h. At this time point there was an increase in the levels of the metabolites saccharopine, aminoadipic acid, and pipecolic acid by 3-, 24- and 3.4-fold, respectively, compared to time zero levels. These metabolites returned to basal levels after 4–6 h. In conclusion, we have developed a LC–MS/MS approach, which allows simultaneous analysis of lysine degradation metabolites without the need for derivatization.
Collapse
Affiliation(s)
- Izabella A Pena
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP Brazil
| | - Lygia A Marques
- Thomson Mass Spectrometry Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-861 Brazil
| | - Angelo B A Laranjeira
- Centro Infantil Boldrini, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-210 Brazil
| | - José A Yunes
- Centro Infantil Boldrini, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-210 Brazil ; Departamento de Genética Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-887 Brazil
| | - Marcos N Eberlin
- Thomson Mass Spectrometry Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-861 Brazil
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP Brazil ; Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970 Brazil
| |
Collapse
|
11
|
Barreto P, Okura V, Pena IA, Maia R, Maia IG, Arruda P. Overexpression of mitochondrial uncoupling protein 1 (UCP1) induces a hypoxic response in Nicotiana tabacum leaves. J Exp Bot 2016; 67:301-13. [PMID: 26494730 PMCID: PMC4682437 DOI: 10.1093/jxb/erv460] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) decreases reactive oxygen species production under stress conditions by uncoupling the electrochemical gradient from ATP synthesis. This study combined transcriptome profiling with experimentally induced hypoxia to mechanistically dissect the impact of Arabidopsis thaliana UCP1 (AtUCP1) overexpression in tobacco. Transcriptomic analysis of AtUCP1-overexpressing (P07) and wild-type (WT) plants was carried out using RNA sequencing. Metabolite and carbohydrate profiling of hypoxia-treated plants was performed using (1)H-nuclear magnetic resonance spectroscopy and high-performance anion-exchange chromatography with pulsed amperometric detection. The transcriptome of P07 plants revealed a broad induction of stress-responsive genes that were not strictly related to the mitochondrial antioxidant machinery, suggesting that overexpression of AtUCP1 imposes a strong stress response within the cell. In addition, transcripts that mapped into carbon fixation and energy expenditure pathways were broadly altered. It was found that metabolite markers of hypoxic adaptation, such as alanine and tricarboxylic acid intermediates, accumulated in P07 plants under control conditions at similar rates to WT plants under hypoxia. These findings indicate that constitutive overexpression of AtUCP1 induces a hypoxic response. The metabolites that accumulated in P07 plants are believed to be important in signalling for an improvement in carbon assimilation and induction of a hypoxic response. Under these conditions, mitochondrial ATP production is less necessary and fermentative glycolysis becomes critical to meet cell energy demands. In this scenario, the more flexible energy metabolism along with an intrinsically activated hypoxic response make these plants better adapted to face several biotic and abiotic stresses.
Collapse
Affiliation(s)
- Pedro Barreto
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil
| | - Vagner Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil
| | - Izabella A Pena
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil
| | - Renato Maia
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil
| | - Ivan G Maia
- Departamento de Genética, Instituto de Biociências, UNESP, 18618-970 Botucatu, SP, Brazil
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP, Brazil
| |
Collapse
|
12
|
Pena IA, Marques LA, Laranjeira ABA, Yunes JA, Eberlin MN, Arruda P. Simultaneous detection of lysine metabolites by a single LC-MS/MS method: monitoring lysine degradation in mouse plasma. Springerplus 2016. [PMID: 27026869 DOI: 10.1186/s40064-016-1809-1801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Detection and quantification of lysine degradation metabolites in plasma is necessary for the diagnosis and follow-up of diseases such as pyridoxine-dependent epilepsy. The principal metabolites involved in the disease are related to the first steps of lysine oxidation, either through the saccharopine or the pipecolate pathways. Currently, there are three different analytical methods used to assess the content of these metabolites in urine and plasma, but they require different sample preparations and analytical equipment. Here, we describe a protocol that calls for a simple sample preparation and uses liquid chromatography tandem mass spectrometry (LC-MS/MS) that allows simultaneous detection and quantification of underivatized l-saccharopine, l-aminoadipic acid, l-pipecolic acid, piperideine-6-carboxylate, l-glutamic acid, and pyridoxal-5-phosphate in plasma samples. To validate the method we analyzed the time course degradation after intraperitoneal injection of l-lysine in C57BL/6/J mice. We observed that the degradation of lysine through the saccharopine pathway reached a maximum within the first 2 h. At this time point there was an increase in the levels of the metabolites saccharopine, aminoadipic acid, and pipecolic acid by 3-, 24- and 3.4-fold, respectively, compared to time zero levels. These metabolites returned to basal levels after 4-6 h. In conclusion, we have developed a LC-MS/MS approach, which allows simultaneous analysis of lysine degradation metabolites without the need for derivatization.
Collapse
Affiliation(s)
- Izabella A Pena
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP Brazil
| | - Lygia A Marques
- Thomson Mass Spectrometry Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-861 Brazil
| | - Angelo B A Laranjeira
- Centro Infantil Boldrini, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-210 Brazil
| | - José A Yunes
- Centro Infantil Boldrini, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-210 Brazil ; Departamento de Genética Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-887 Brazil
| | - Marcos N Eberlin
- Thomson Mass Spectrometry Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-861 Brazil
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875 Campinas, SP Brazil ; Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970 Brazil
| |
Collapse
|
13
|
Fernandes GR, Barbosa DVC, Prosdocimi F, Pena IA, Santana-Santos L, Coelho Junior O, Barbosa-Silva A, Velloso HM, Mudado MA, Natale DA, Faria-Campos AC, Aguiar SCV, Ortega JM. A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model. Genet Mol Res 2008; 7:910-24. [PMID: 18949709 DOI: 10.4238/vol7-3x-meeting008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A procedure to recruit members to enlarge protein family databases is described here. The procedure makes use of UniRef50 clusters produced by UniProt. Current family entries are used to recruit additional members based on the UniRef50 clusters to which they belong. Only those additional UniRef50 members that are not fragments and whose length is within a restricted range relative to the original entry are recruited. The enriched dataset is then limited to contain only genomes from selected clades. We used the COG database - used for genome annotation and for studies of phylogenetics and gene evolution - as a model. To validate the method, a UniRef-Enriched COG0151 (UECOG) was tested with distinct procedures to compare recruited members with the recruiters: PSI-BLAST, secondary structure overlap (SOV), Seed Linkage, COGnitor, shared domain content, and neighbor-joining single-linkage, and observed that the former four agree in their validations. Presently, the UniRef50-based recruitment procedure enriches the COG database for Archaea, Bacteria and its subgroups Actinobacteria, Firmicutes, Proteobacteria, and other bacteria by 2.2-, 8.0-, 7.0-, 8.8-, 8.7-, and 4.2-fold, respectively, in terms of sequences, and also considerably increased the number of species.
Collapse
Affiliation(s)
- G R Fernandes
- Departamento de Bioquímica e Imunologia, Laboratório de Biodados, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|