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Kühnisch J, Theisen S, Dartsch J, Fritsche-Guenther R, Kirchner M, Obermayer B, Bauer A, Kahlert AK, Rothe M, Beule D, Heuser A, Mertins P, Kirwan JA, Berndt N, MacRae CA, Hubner N, Klaassen S. Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators. Cardiovasc Res 2024; 119:2902-2916. [PMID: 37842925 PMCID: PMC10874277 DOI: 10.1093/cvr/cvad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 10/17/2023] Open
Abstract
AIMS Mutation of the PRDM16 gene causes human dilated and non-compaction cardiomyopathy. The PRDM16 protein is a transcriptional regulator that affects cardiac development via Tbx5 and Hand1, thus regulating myocardial structure. The biallelic inactivation of Prdm16 induces severe cardiac dysfunction with post-natal lethality and hypertrophy in mice. The early pathological events that occur upon Prdm16 inactivation have not been explored. METHODS AND RESULTS This study performed in-depth pathophysiological and molecular analyses of male and female Prdm16csp1/wt mice that carry systemic, monoallelic Prdm16 gene inactivation. We systematically assessed early molecular changes through transcriptomics, proteomics, and metabolomics. Kinetic modelling of cardiac metabolism was performed in silico with CARDIOKIN. Prdm16csp1/wt mice are viable up to 8 months, develop hypoplastic hearts, and diminished systolic performance that is more pronounced in female mice. Prdm16csp1/wt cardiac tissue of both sexes showed reductions in metabolites associated with amino acid as well as glycerol metabolism, glycolysis, and the tricarboxylic acid cycle. Prdm16csp1/wt cardiac tissue revealed diminished glutathione (GSH) and increased inosine monophosphate (IMP) levels indicating oxidative stress and a dysregulated energetics, respectively. An accumulation of triacylglycerides exclusively in male Prdm16csp1/wt hearts suggests a sex-specific metabolic adaptation. Metabolic modelling using CARDIOKIN identified a reduction in fatty acid utilization in males as well as lower glucose utilization in female Prdm16csp1/wt cardiac tissue. On the level of transcripts and protein expression, Prdm16csp1/wt hearts demonstrate an up-regulation of pyridine nucleotide-disulphide oxidoreductase domain 2 (Pyroxd2) and the transcriptional regulator pre-B-cell leukaemia transcription factor interacting protein 1 (Pbxip1). The strongest concordant transcriptional up-regulation was detected for Prdm16 itself, probably through an autoregulatory mechanism. CONCLUSIONS Monoallelic, global Prdm16 mutation diminishes cardiac performance in Prdm16csp1/wt mice. Metabolic alterations and transcriptional dysregulation in Prdm16csp1/wt affect cardiac tissue. Female Prdm16csp1/wt mice develop a more pronounced phenotype, indicating sexual dimorphism at this early pathological window. This study suggests that metabolic dysregulation is an early event in the PRDM16 associated cardiac pathology.
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Affiliation(s)
- Jirko Kühnisch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Simon Theisen
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Josephine Dartsch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Raphaela Fritsche-Guenther
- BIH Metabolomics Platform, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marieluise Kirchner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Bauer
- BIH Metabolomics Platform, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- DZHK German Center for Cardiovascular Research, partner site Hamburg/Kiel/Lübeck, Germany
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | | | - Dieter Beule
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Arnd Heuser
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Philipp Mertins
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jennifer A Kirwan
- BIH Metabolomics Platform, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nikolaus Berndt
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Computer-assisted Cardiovascular Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam—Rehbruecke (DIfE), Nuthetal, Germany
| | - Calum A MacRae
- Harvard Medical School and Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, USA
| | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Sabine Klaassen
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Pediatric Cardiology, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
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2
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Amarasekera SSC, Hock DH, Lake NJ, Calvo SE, Grønborg SW, Krzesinski EI, Amor DJ, Fahey MC, Simons C, Wibrand F, Mootha VK, Lek M, Lunke S, Stark Z, Østergaard E, Christodoulou J, Thorburn DR, Stroud DA, Compton AG. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease. Hum Mol Genet 2023; 32:2441-2454. [PMID: 37133451 PMCID: PMC10360397 DOI: 10.1093/hmg/ddad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
MRPL39 encodes one of 52 proteins comprising the large subunit of the mitochondrial ribosome (mitoribosome). In conjunction with 30 proteins in the small subunit, the mitoribosome synthesizes the 13 subunits of the mitochondrial oxidative phosphorylation (OXPHOS) system encoded by mitochondrial Deoxyribonucleic acid (DNA). We used multi-omics and gene matching to identify three unrelated individuals with biallelic variants in MRPL39 presenting with multisystem diseases with severity ranging from lethal, infantile-onset (Leigh syndrome spectrum) to milder with survival into adulthood. Clinical exome sequencing of known disease genes failed to diagnose these patients; however quantitative proteomics identified a specific decrease in the abundance of large but not small mitoribosomal subunits in fibroblasts from the two patients with severe phenotype. Re-analysis of exome sequencing led to the identification of candidate single heterozygous variants in mitoribosomal genes MRPL39 (both patients) and MRPL15. Genome sequencing identified a shared deep intronic MRPL39 variant predicted to generate a cryptic exon, with transcriptomics and targeted studies providing further functional evidence for causation. The patient with the milder disease was homozygous for a missense variant identified through trio exome sequencing. Our study highlights the utility of quantitative proteomics in detecting protein signatures and in characterizing gene-disease associations in exome-unsolved patients. We describe Relative Complex Abundance analysis of proteomics data, a sensitive method that can identify defects in OXPHOS disorders to a similar or greater sensitivity to the traditional enzymology. Relative Complex Abundance has potential utility for functional validation or prioritization in many hundreds of inherited rare diseases where protein complex assembly is disrupted.
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Affiliation(s)
- Sumudu S C Amarasekera
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole J Lake
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Sabine W Grønborg
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Center for Inherited Metabolic Disease, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Emma I Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - David J Amor
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael C Fahey
- Monash Genetics, Monash Health, Melbourne, VIC 3168 Australia
- Department of Paediatrics, Monash University, Melbourne, VIC 3168 Australia
| | - Cas Simons
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flemming Wibrand
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02446, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Department of Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen 2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - John Christodoulou
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - David R Thorburn
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - David A Stroud
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Alison G Compton
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
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3
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Kambali M, Li Y, Unichenko P, Pliego JF, Yadav R, Liu J, McGuinness P, Cobb JG, Wang M, Nagarajan R, Lyu J, Vongsouthi V, Jackson CJ, Engin E, Coyle JT, Shin J, Talkowski ME, Homanics GE, Bolshakov VY, Henneberger C, Rudolph U. A marker chromosome in psychosis identifies glycine decarboxylase (GLDC) as a novel regulator of neuronal and synaptic function in the hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542745. [PMID: 37398055 PMCID: PMC10312439 DOI: 10.1101/2023.05.29.542745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The biological significance of a small supernumerary marker chromosome that results in dosage alterations to chromosome 9p24.1, including triplication of the GLDC gene encoding glycine decarboxylase, in two patients with psychosis is unclear. In an allelic series of copy number variant mouse models, we identify that triplication of Gldc reduces extracellular glycine levels as determined by optical fluorescence resonance energy transfer (FRET) in dentate gyrus (DG) but not in CA1, suppresses long-term potentiation (LTP) in mPP-DG synapses but not in CA3-CA1 synapses, reduces the activity of biochemical pathways implicated in schizophrenia and mitochondrial bioenergetics, and displays deficits in prepulse inhibition, startle habituation, latent inhibition, working memory, sociability and social preference. Our results thus provide a link between a genomic copy number variation, biochemical, cellular and behavioral phenotypes, and further demonstrate that GLDC negatively regulates long-term synaptic plasticity at specific hippocampal synapses, possibly contributing to the development of neuropsychiatric disorders.
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Van Bergen NJ, Gunanayagam K, Bournazos AM, Walvekar AS, Warmoes MO, Semcesen LN, Lunke S, Bommireddipalli S, Sikora T, Patraskaki M, Jones DL, Garza D, Sebire D, Gooley S, McLean CA, Naidoo P, Rajasekaran M, Stroud DA, Linster CL, Wallis M, Cooper ST, Christodoulou J. Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma. Int J Mol Sci 2023; 24:ijms24043582. [PMID: 36834994 PMCID: PMC9963268 DOI: 10.3390/ijms24043582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
We have previously reported that pathogenic variants in a key metabolite repair enzyme NAXD cause a lethal neurodegenerative condition triggered by episodes of fever in young children. However, the clinical and genetic spectrum of NAXD deficiency is broadening as our understanding of the disease expands and as more cases are identified. Here, we report the oldest known individual succumbing to NAXD-related neurometabolic crisis, at 32 years of age. The clinical deterioration and demise of this individual were likely triggered by mild head trauma. This patient had a novel homozygous NAXD variant [NM_001242882.1:c.441+3A>G:p.?] that induces the mis-splicing of the majority of NAXD transcripts, leaving only trace levels of canonically spliced NAXD mRNA, and protein levels below the detection threshold by proteomic analysis. Accumulation of damaged NADH, the substrate of NAXD, could be detected in the fibroblasts of the patient. In agreement with prior anecdotal reports in paediatric patients, niacin-based treatment also partly alleviated some clinical symptoms in this adult patient. The present study extends our understanding of NAXD deficiency by uncovering shared mitochondrial proteomic signatures between the adult and our previously reported paediatric NAXD cases, with reduced levels of respiratory complexes I and IV as well as the mitoribosome, and the upregulation of mitochondrial apoptotic pathways. Importantly, we highlight that head trauma in adults, in addition to paediatric fever or illness, may precipitate neurometabolic crises associated with pathogenic NAXD variants.
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Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Correspondence: (N.J.V.B.); (J.C.)
| | - Karen Gunanayagam
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Adam M. Bournazos
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
| | - Adhish S. Walvekar
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Marc O. Warmoes
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Liana N. Semcesen
- Department of Biochemistry & Pharmacology, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Sebastian Lunke
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
| | - Tim Sikora
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
| | - Myrto Patraskaki
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Dean L. Jones
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Denisse Garza
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Dale Sebire
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Samuel Gooley
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Catriona A. McLean
- Department of Anatomical Pathology, Alfred Hospital, Melbourne, VIC 3002, Australia
| | - Parm Naidoo
- Department of Medical Imaging, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Mugil Rajasekaran
- Department of Medical Imaging, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - David A. Stroud
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Biochemistry & Pharmacology, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Carole L. Linster
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Mathew Wallis
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
- Correspondence: (N.J.V.B.); (J.C.)
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