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Chen Y, Dawes R, Kim HC, Stenton SL, Walker S, Ljungdahl A, Lord J, Ganesh VS, Ma J, Martin-Geary AC, Lemire G, D'Souza EN, Dong S, Ellingford JM, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Brown NJ, Burrage LC, Chapman K, Compton AG, Cunningham CA, D'Souza P, Délot EC, Dias KR, Elias ER, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Grant CL, Haack T, Kuechler A, Lalani SR, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lockhart PJ, Ma AS, Macnamara EF, Maurer TM, Mendez HR, Montgomery SB, Nassogne MC, Neumann S, O'Leary M, Palmer EE, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Simons C, Sisodiya SM, Snell P, Clair LS, Stark Z, Tan TY, Tan NB, Temple SE, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JM, Sanders SJ, O'Donnell-Luria A, Whiffin N. De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. medRxiv 2024:2024.04.07.24305438. [PMID: 38645094 PMCID: PMC11030480 DOI: 10.1101/2024.04.07.24305438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome 2 . We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2 's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.
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Baker MJ, Blau KU, Anderson AJ, Palmer CS, Fielden LF, Crameri JJ, Milenkovic D, Thorburn DR, Frazier AE, Langer T, Stojanovski D. CLPB disaggregase dysfunction impacts the functional integrity of the proteolytic SPY complex. J Cell Biol 2024; 223:e202305087. [PMID: 38270563 PMCID: PMC10818064 DOI: 10.1083/jcb.202305087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/07/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
CLPB is a mitochondrial intermembrane space AAA+ domain-containing disaggregase. CLPB mutations are associated with 3-methylglutaconic aciduria and neutropenia; however, the molecular mechanism underscoring disease and the contribution of CLPB substrates to disease pathology remains unknown. Interactions between CLPB and mitochondrial quality control (QC) factors, including PARL and OPA1, have been reported, hinting at dysregulation of organelle QC in disease. Utilizing proteomic and biochemical approaches, we show a stress-specific aggregation phenotype in a CLPB-null environment and define the CLPB substrate profile. We illustrate an interplay between intermembrane space proteins including CLPB, HAX1, HTRA2, and the inner membrane quality control proteins (STOML2, PARL, YME1L1; SPY complex), with CLPB deficiency impeding SPY complex function by virtue of protein aggregation in the intermembrane space. We conclude that there is an interdependency of mitochondrial QC components at the intermembrane space/inner membrane interface, and perturbations to this network may underscore CLPB disease pathology.
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Affiliation(s)
- Megan J. Baker
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Kai Uwe Blau
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Alexander J. Anderson
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Catherine S. Palmer
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Laura F. Fielden
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Dusanka Milenkovic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - David R. Thorburn
- Royal Children’s Hospital and Department of Paediatrics, Murdoch Children’s Research Institute, The University of Melbourne, Parkville, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Parkville, Australia
| | - Ann E. Frazier
- Royal Children’s Hospital and Department of Paediatrics, Murdoch Children’s Research Institute, The University of Melbourne, Parkville, Australia
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
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Missen S, Wilson C, Potter H, Vincent AL, Murphy R, Roxburgh R, Rodrigues M, Poke G, Robertson SP, Thorburn DR, Glamuzina E. Mitochondrial disease in New Zealand: a nationwide prevalence study. Intern Med J 2024; 54:388-397. [PMID: 37732891 DOI: 10.1111/imj.16211] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND The complexities of mitochondrial disease make epidemiological studies challenging, yet this information is important in understanding the healthcare burden and addressing service and educational needs. Existing studies are limited to quaternary centres or focus on a single genotype or phenotype and estimate disease prevalence at 12.5 per 100 000. New Zealand's (NZ) size and partially integrated national healthcare system make it amenable to a nationwide prevalence study. AIM To estimate the prevalence of molecularly confirmed and suspected mitochondrial disease on 31 December 2015 in NZ. METHODS Cases were identified from subspecialists and laboratory databases and through interrogation of the Ministry of Health National Minimum Dataset with a focus on presentations between 2000 and 2015. Patient records were reviewed, and those with a diagnosis of 'mitochondrial disease' who were alive and residing in NZ on the prevalence date were included. These were divided into molecularly confirmed and clinically suspected cases. Official NZ estimated resident population data were used to calculate prevalence. RESULTS Seven hundred twenty-three unique national health index numbers were identified. Five hundred five were excluded. The minimum combined prevalence for mitochondrial disease was 4.7 per 100 000 (95% confidence interval (CI): 4.1-5.4). The minimum prevalence for molecularly confirmed and suspected disease was 2.9 (95% CI 2.4-3.4) and 1.8 (95% CI 1.4-2.2) cases per 100 000 respectively. CONCLUSIONS Within the limitations of this study, comparison to similar prevalence studies performed by specialist referral centres suggests mitochondrial disease is underdiagnosed in NZ. This highlights a need for improved education and referral pathways for mitochondrial disease in NZ.
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Affiliation(s)
- Sarah Missen
- Child Health Service, Whangarei Hospital, Te Whatu Ora - Health New Zealand, Te Tai Tokerau, Whangarei, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Callum Wilson
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Adult and Paediatric National Metabolic Service, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
| | - Howard Potter
- Canterbury Health Labs, Te Whatu Ora - Health New Zealand, Waitaha Canterbury, Christchurch, New Zealand
| | - Andrea L Vincent
- Greenlane Eye Clinic, Greenlane Clinical Centre, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Rinki Murphy
- Auckland Diabetes Centre, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Te Mana Ki Tua, Specialist Weight Management Service, Middlemore Hospital, Te Whatu Ora - Health New Zealand, Counties Manukau, Auckland, New Zealand
| | - Richard Roxburgh
- Department of Neurology, Auckland City Hospital, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Centre for Brain Research, Neurogenetics Clinics, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Miriam Rodrigues
- Department of Neurology, Auckland City Hospital, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Centre for Brain Research, Neurogenetics Clinics, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Gemma Poke
- Central Hub, Genetic Health Service New Zealand, Te Whatu Ora - Health New Zealand, Wellington, New Zealand
| | | | - David R Thorburn
- Genomic Medicine Theme, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Emma Glamuzina
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Adult and Paediatric National Metabolic Service, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
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6
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Vogel GF, Mozer-Glassberg Y, Landau YE, Schlieben LD, Prokisch H, Feichtinger RG, Mayr JA, Brennenstuhl H, Schröter J, Pechlaner A, Alkuraya FS, Baker JJ, Barcia G, Baric I, Braverman N, Burnyte B, Christodoulou J, Ciara E, Coman D, Das AM, Darin N, Della Marina A, Distelmaier F, Eklund EA, Ersoy M, Fang W, Gaignard P, Ganetzky RD, Gonzales E, Howard C, Hughes J, Konstantopoulou V, Kose M, Kerr M, Khan A, Lenz D, McFarland R, Margolis MG, Morrison K, Müller T, Murayama K, Nicastro E, Pennisi A, Peters H, Piekutowska-Abramczuk D, Rötig A, Santer R, Scaglia F, Schiff M, Shagrani M, Sharrard M, Soler-Alfonso C, Staufner C, Storey I, Stormon M, Taylor RW, Thorburn DR, Teles EL, Wang JS, Weghuber D, Wortmannd S. Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants. Genet Med 2023; 25:100828. [PMID: 37272928 DOI: 10.1016/j.gim.2023.100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
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7
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Bakhshalizadeh S, Hock DH, Siddall NA, Kline BL, Sreenivasan R, Bell KM, Casagranda F, Kamalanathan S, Sahoo J, Narayanan N, Naik D, Suryadevara V, Compton AG, Amarasekera SSC, Kapoor R, Jaillard S, Simpson A, Robevska G, van den Bergen J, Pachernegg S, Ayers KL, Thorburn DR, Stroud DA, Hime GR, Sinclair AH, Tucker EJ. Deficiency of the mitochondrial ribosomal subunit, MRPL50, causes autosomal recessive syndromic premature ovarian insufficiency. Hum Genet 2023:10.1007/s00439-023-02563-z. [PMID: 37148394 DOI: 10.1007/s00439-023-02563-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/19/2023] [Indexed: 05/08/2023]
Abstract
Premature ovarian insufficiency (POI) is a common cause of infertility in women, characterised by amenorrhea and elevated FSH under the age of 40 years. In some cases, POI is syndromic in association with other features such as sensorineural hearing loss in Perrault syndrome. POI is a heterogeneous disease with over 80 causative genes known so far; however, these explain only a minority of cases. Using whole-exome sequencing (WES), we identified a MRPL50 homozygous missense variant (c.335T > A; p.Val112Asp) shared by twin sisters presenting with POI, bilateral high-frequency sensorineural hearing loss, kidney and heart dysfunction. MRPL50 encodes a component of the large subunit of the mitochondrial ribosome. Using quantitative proteomics and western blot analysis on patient fibroblasts, we demonstrated a loss of MRPL50 protein and an associated destabilisation of the large subunit of the mitochondrial ribosome whilst the small subunit was preserved. The mitochondrial ribosome is responsible for the translation of subunits of the mitochondrial oxidative phosphorylation machinery, and we found patient fibroblasts have a mild but significant decrease in the abundance of mitochondrial complex I. These data support a biochemical phenotype associated with MRPL50 variants. We validated the association of MRPL50 with the clinical phenotype by knockdown/knockout of mRpL50 in Drosophila, which resulted abnormal ovarian development. In conclusion, we have shown that a MRPL50 missense variant destabilises the mitochondrial ribosome, leading to oxidative phosphorylation deficiency and syndromic POI, highlighting the importance of mitochondrial support in ovarian development and function.
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Affiliation(s)
- Shabnam Bakhshalizadeh
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | | | - Rajini Sreenivasan
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katrina M Bell
- Department of Bioinformatics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Franca Casagranda
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | - Sadishkumar Kamalanathan
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Jayaprakash Sahoo
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Niya Narayanan
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Dukhabandhu Naik
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Varun Suryadevara
- Department of Endocrinology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, 605006, India
| | - Alison G Compton
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ridam Kapoor
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
| | - Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000, Rennes, France
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033, Rennes, France
| | - Andrea Simpson
- School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC, Australia
- College of Health and Human Services, Charles Darwin University, Darwin, NT, Australia
| | | | | | - Svenja Pachernegg
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katie L Ayers
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - David A Stroud
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia.
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.
| | - Elena J Tucker
- Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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8
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Poquérusse J, Nolan M, Thorburn DR, Van Hove JLK, Friederich MW, Love DR, Taylor J, Powell CA, Minczuk M, Snell RG, Lehnert K, Glamuzina E, Jacobsen JC. Severe neonatal onset neuroregression with paroxysmal dystonia and apnoea: Expanding the phenotypic and genotypic spectrum of CARS2-related mitochondrial disease. JIMD Rep 2023; 64:223-232. [PMID: 37151360 PMCID: PMC10159863 DOI: 10.1002/jmd2.12360] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Disorders of mitochondrial function are a collectively common group of genetic diseases in which deficits in core mitochondrial translation machinery, including aminoacyl tRNA synthetases, are key players. Biallelic variants in the CARS2 gene (NM_024537.4), which encodes the mitochondrial aminoacyl-tRNA synthetase for cysteine (CARS2, mt-aaRScys; MIM*612800), result in childhood onset epileptic encephalopathy and complex movement disorder with combined oxidative phosphorylation deficiency (MIM#616672). Prior to this report, eight unique pathogenic variants in the CARS2 gene had been reported in seven individuals. Here, we describe a male who presented in the third week of life with apnoea. He rapidly deteriorated with paroxysmal dystonic crises and apnoea resulting in death at 16 weeks. He had no evidence of seizure activity or multisystem disease and had normal brain imaging. Skeletal muscle biopsy revealed a combined disorder of oxidative phosphorylation. Whole-exome sequencing identified biallelic variants in the CARS2 gene: one novel (c.1478T>C, p.Phe493Ser), and one previously reported (c.655G>A, p.Ala219Thr; rs727505361). Northern blot analysis of RNA isolated from the patient's fibroblasts confirmed a clear defect in aminoacylation of the mitochondrial tRNA for cysteine (mt-tRNACys). To our knowledge, this is the earliest reported case of CARS2 deficiency with severe, early onset dystonia and apnoea, without epilepsy.
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Affiliation(s)
- Jessie Poquérusse
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Melinda Nolan
- Department of NeurologyStarship Children's HealthAucklandNew Zealand
| | - David R. Thorburn
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsThe University of MelbourneMelbourneVictoriaAustralia
| | - Johan L. K. Van Hove
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Marisa W. Friederich
- Department of Pediatrics, School of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of Pathology and Laboratory MedicineChildren's Hospital ColoradoAuroraColoradoUSA
| | - Donald R. Love
- Diagnostic GeneticsLabPLUS, Auckland City HospitalAucklandNew Zealand
- Present address:
Division Chief, Pathology GeneticsSidra MedicineDohaQatar
| | - Juliet Taylor
- Genetic Health Service New ZealandAuckland City HospitalAucklandNew Zealand
| | | | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Russell G. Snell
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Klaus Lehnert
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic ServiceAuckland City HospitalAucklandNew Zealand
| | - Jessie C. Jacobsen
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
- Centre for Brain ResearchThe University of AucklandAucklandNew Zealand
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9
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Kiss S, Christodoulou J, Thorburn DR, Freeman JL, Kornberg AJ, Mandelstam S, Compton AG, Cummings B, Pais L, Yaplito-Lee J, White SM. A cryptic pathogenic NDUFV1 variant identified by RNA-seq in a patient with normal complex I activity in muscle and transient magnetic resonance imaging changes. Am J Med Genet A 2023; 191:1599-1606. [PMID: 36896486 DOI: 10.1002/ajmg.a.63170] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/18/2023] [Accepted: 02/15/2023] [Indexed: 03/11/2023]
Abstract
Mitochondrial respiratory chain disorders (MRC) are amongst the most common group of inborn errors of metabolism. MRC, of which complex I deficiency accounts for approximately a quarter, are very diverse, causing a wide range of clinical problems and can be difficult to diagnose. We report an illustrative MRC case whose diagnosis was elusive. Clinical signs included failure to thrive caused by recurrent vomiting, hypotonia and progressive loss of motor milestones. Initial brain imaging suggested Leigh syndrome but without expected diffusion restriction. Muscle respiratory chain enzymology was unremarkable. Whole-genome sequencing identified a maternally inherited NDUFV1 missense variant [NM_007103.4 (NDUFV1):c.1157G > A; p.(Arg386His)] and a paternally inherited synonymous variant [NM_007103.4 (NDUFV1):c.1080G > A; (p.Ser360=)]. RNA sequencing demonstrated aberrant splicing. This case emphasizes the diagnostic odyssey of a patient in whom a confirmed diagnosis was elusive because of atypical features and normal muscle respiratory chain enzyme (RCE) activities, along with a synonymous variant, which are often filtered out from genomic analyses. It also illustrates the following points: (1) complete resolution of magnetic resonance imaging changes may be part of the picture in mitochondrial disease; (2) analysis for synonymous variants is important for undiagnosed patients; and (3) RNA-seq is a powerful tool to demonstrate pathogenicity of putative splicing variants.
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Affiliation(s)
- Sharmila Kiss
- Department of Metabolic Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - John Christodoulou
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Murdoch, Victoria, Australia
| | - David R Thorburn
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Murdoch, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Jeremy L Freeman
- Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Andrew J Kornberg
- Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Simone Mandelstam
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Radiology, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Alison G Compton
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Murdoch, Victoria, Australia
| | - Beryl Cummings
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Joy Yaplito-Lee
- Department of Metabolic Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
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10
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Stark Z, Boughtwood T, Haas M, Braithwaite J, Gaff CL, Goranitis I, Spurdle AB, Hansen DP, Hofmann O, Laing N, Metcalfe S, Newson AJ, Scott HS, Thorne N, Ward RL, Dinger ME, Best S, Long JC, Grimmond SM, Pearson J, Waddell N, Barnett CP, Cook M, Field M, Fielding D, Fox SB, Gecz J, Jaffe A, Leventer RJ, Lockhart PJ, Lunke S, Mallett AJ, McGaughran J, Mileshkin L, Nones K, Roscioli T, Scheffer IE, Semsarian C, Simons C, Thomas DM, Thorburn DR, Tothill R, White D, Dunwoodie S, Simpson PT, Phillips P, Brion MJ, Finlay K, Quinn MC, Mattiske T, Tudini E, Boggs K, Murray S, Wells K, Cannings J, Sinclair AH, Christodoulou J, North KN. Australian Genomics: Outcomes of a 5-year national program to accelerate the integration of genomics in healthcare. Am J Hum Genet 2023; 110:419-426. [PMID: 36868206 PMCID: PMC10027474 DOI: 10.1016/j.ajhg.2023.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
Australian Genomics is a national collaborative partnership of more than 100 organizations piloting a whole-of-system approach to integrating genomics into healthcare, based on federation principles. In the first five years of operation, Australian Genomics has evaluated the outcomes of genomic testing in more than 5,200 individuals across 19 rare disease and cancer flagship studies. Comprehensive analyses of the health economic, policy, ethical, legal, implementation and workforce implications of incorporating genomics in the Australian context have informed evidence-based change in policy and practice, resulting in national government funding and equity of access for a range of genomic tests. Simultaneously, Australian Genomics has built national skills, infrastructure, policy, and data resources to enable effective data sharing to drive discovery research and support improvements in clinical genomic delivery.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Childhood Dementia Initiative, Sydney, NSW, Australia
| | - Matilda Haas
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; International Society for Quality in Health Care, Dublin, Ireland
| | - Clara L Gaff
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David P Hansen
- Australian e-Health Research Centre, CSIRO Health and Biosecurity, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Oliver Hofmann
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Sylvia Metcalfe
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ainsley J Newson
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, Sydney, NSW, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Natalie Thorne
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Robyn L Ward
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - John Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Matthew Cook
- Centre for Personalised Immunology, Australian National University, Canberra, ACT, Australia; Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, UK
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Newcastle, NSW, Australia
| | - David Fielding
- Department of Thoracic Medicine, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia
| | - Richard J Leventer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Paul J Lockhart
- University of Melbourne, Melbourne, VIC, Australia; Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Mallett
- KidGen Collaborative, Australian Genomics, Melbourne, VIC, Australia; Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia; School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Katia Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, UNSW, Sydney, NSW, Australia
| | - Ingrid E Scheffer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia; Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Christopher Semsarian
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Cas Simons
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Richard Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Deborah White
- Blood Cancer Program, Precision Cancer Medicine Theme, The South Australian Medical Research Institute, Adelaide, SA, Australia; Faculty of Health and Medical Science, The University of Adelaide, Adelaide, SA, Australia
| | - Sally Dunwoodie
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Peta Phillips
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Marie-Jo Brion
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Keri Finlay
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael Cj Quinn
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Tessa Mattiske
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Emma Tudini
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kirsten Boggs
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia; Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Sean Murray
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Mito Foundation, Sydney, NSW, Australia
| | - Kathy Wells
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Breast Cancer Network Australia, Melbourne, VIC, Australia
| | - John Cannings
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Thoracic Oncology Group of Australasia, Melbourne, VIC, Australia; ProCan, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Andrew H Sinclair
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - John Christodoulou
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Kathryn N North
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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11
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Van Haute L, O'Connor E, Díaz-Maldonado H, Munro B, Polavarapu K, Hock DH, Arunachal G, Athanasiou-Fragkouli A, Bardhan M, Barth M, Bonneau D, Brunetti-Pierri N, Cappuccio G, Caruana NJ, Dominik N, Goel H, Helman G, Houlden H, Lenaers G, Mention K, Murphy D, Nandeesh B, Olimpio C, Powell CA, Preethish-Kumar V, Procaccio V, Rius R, Rebelo-Guiomar P, Simons C, Vengalil S, Zaki MS, Ziegler A, Thorburn DR, Stroud DA, Maroofian R, Christodoulou J, Gustafsson C, Nalini A, Lochmüller H, Minczuk M, Horvath R. TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease. Nat Commun 2023; 14:1009. [PMID: 36823193 PMCID: PMC9950373 DOI: 10.1038/s41467-023-36277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.
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Affiliation(s)
- Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Héctor Díaz-Maldonado
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Benjamin Munro
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Gautham Arunachal
- Department of Human genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Alkyoni Athanasiou-Fragkouli
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Magalie Barth
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Natalia Dominik
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Himanshu Goel
- Hunter Genetics, Waratah, University of Newcastle, Callaghan, NSW, 2298, Australia
| | - Guy Helman
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Henry Houlden
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Guy Lenaers
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Karine Mention
- Pediatric Inherited Metabolic Disorders, Hôpital Jeanne de Flandre, Lille, France
| | - David Murphy
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Bevinahalli Nandeesh
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Catarina Olimpio
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Vincent Procaccio
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Rocio Rius
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Cas Simons
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Alban Ziegler
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - David R Thorburn
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Reza Maroofian
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Claes Gustafsson
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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12
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Thompson K, Stroud DA, Thorburn DR, Taylor RW. Investigation of oxidative phosphorylation activity and complex composition in mitochondrial disease. Handb Clin Neurol 2023; 194:127-139. [PMID: 36813309 DOI: 10.1016/b978-0-12-821751-1.00008-7] [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] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A multidisciplinary approach to the laboratory diagnosis of mitochondrial disease has long been applied, with crucial information provided by deep clinical phenotyping, blood investigations, and biomarker screening as well as histopathological and biochemical testing of biopsy material to support molecular genetic screening. In an era of second and third generation sequencing technologies, traditional diagnostic algorithms for mitochondrial disease have been replaced by gene agnostic, genomic strategies including whole-exome sequencing (WES) and whole-genome sequencing (WGS), increasingly supported by other 'omics technologies (Alston et al., 2021). Whether a primary testing strategy, or one used to validate and interpret candidate genetic variants, the availability of a range of tests aimed at determining mitochondrial function (i.e., the assessment of individual respiratory chain enzyme activities in a tissue biopsy or cellular respiration in a patient cell line) remains an important part of the diagnostic armory. In this chapter, we summarize several disciplines used in the laboratory investigation of suspected mitochondrial disease, including the histopathological and biochemical assessment of mitochondrial function, as well as protein-based techniques to assess the steady-state levels of oxidative phosphorylation (OXPHOS) subunits and assembly of OXPHOS complexes via traditional (immunoblotting) and cutting-edge (quantitative proteomic) approaches.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia; Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Mitochondrial Laboratory, Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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13
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Baker MJ, Crameri JJ, Thorburn DR, Frazier AE, Stojanovski D. Mitochondrial biology and dysfunction in secondary mitochondrial disease. Open Biol 2022; 12:220274. [PMID: 36475414 PMCID: PMC9727669 DOI: 10.1098/rsob.220274] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.
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Affiliation(s)
- Megan J. Baker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia,Victorian Clinical Genetics Services, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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14
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Rius R, Bennett NK, Bhattacharya K, Riley LG, Yüksel Z, Formosa LE, Compton AG, Dale RC, Cowley MJ, Gayevskiy V, Al Tala SM, Almehery AA, Ryan MT, Thorburn DR, Nakamura K, Christodoulou J. Biallelic pathogenic variants in COX11 are associated with an infantile-onset mitochondrial encephalopathy. Hum Mutat 2022; 43:1970-1978. [PMID: 36030551 PMCID: PMC9771894 DOI: 10.1002/humu.24453] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/20/2022] [Revised: 07/28/2022] [Accepted: 08/22/2022] [Indexed: 01/25/2023]
Abstract
Primary mitochondrial diseases are a group of genetically and clinically heterogeneous disorders resulting from oxidative phosphorylation (OXPHOS) defects. COX11 encodes a copper chaperone that participates in the assembly of complex IV and has not been previously linked to human disease. In a previous study, we identified that COX11 knockdown decreased cellular adenosine triphosphate (ATP) derived from respiration, and that ATP levels could be restored with coenzyme Q10 (CoQ10 ) supplementation. This finding is surprising since COX11 has no known role in CoQ10 biosynthesis. Here, we report a novel gene-disease association by identifying biallelic pathogenic variants in COX11 associated with infantile-onset mitochondrial encephalopathies in two unrelated families using trio genome and exome sequencing. Functional studies showed that mutant COX11 fibroblasts had decreased ATP levels which could be rescued by CoQ10 . These results not only suggest that COX11 variants cause defects in energy production but reveal a potential metabolic therapeutic strategy for patients with COX11 variants.
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Affiliation(s)
- Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - Neal K. Bennett
- Gladstone Institute of Neurological DiseaseGladstone InstitutesSan FranciscoCaliforniaUSA
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders ServiceThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Genetic Medicine, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
| | - Lisa G. Riley
- Specialty of Child & Adolescent HealthUniversity of SydneySydneyAustralia
- Rare Diseases Functional GenomicsThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
| | - Zafer Yüksel
- Department of Human GeneticsBioscientia Healthcare GmbHIngelheimGermany
| | - Luke E. Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Alison G. Compton
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
| | - Russell C. Dale
- Department of Paediatric Neurology and Clinical school, The Children's Hospital at Westmead, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Mark J. Cowley
- Children's Cancer Institute & School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical GenomicsGarvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Saeed M. Al Tala
- Pediatric DirectorateNeonatal NICU, Armed Forces Hospital SRKhamis MushaytSaudi Arabia
| | | | - Michael T. Ryan
- Department of Human GeneticsBioscientia Healthcare GmbHIngelheimGermany
| | - David R. Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
- Victorian Clinical Genetics ServicesRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Ken Nakamura
- Gladstone Institute of Neurological DiseaseGladstone InstitutesSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Graduate Programs in Biomedical Sciences and NeuroscienceUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research InstituteRoyal Children's HospitalMelbourneAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneAustralia
- Discipline of Genetic Medicine, Sydney Medical SchoolUniversity of SydneySydneyNew South WalesAustralia
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15
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Vogel GF, Mozer-Glassberg Y, Landau YE, Schlieben LD, Prokisch H, Feichtinger RG, Mayr JA, Brennenstuhl H, Schröter J, Pechlaner A, Alkuraya FS, Baker JJ, Barcia G, Baric I, Braverman N, Burnyte B, Christodoulou J, Ciara E, Coman D, Das AM, Darin N, Della Marina A, Distelmaier F, Eklund EA, Ersoy M, Fang W, Gaignard P, Ganetzky RD, Gonzales E, Howard C, Hughes J, Konstantopoulou V, Kose M, Kerr M, Khan A, Lenz D, McFarland R, Margolis MG, Morrison K, Müller T, Murayama K, Nicastro E, Pennisi A, Peters H, Piekutowska-Abramczuk D, Rötig A, Santer R, Scaglia F, Schiff M, Shagrani M, Sharrard M, Soler-Alfonso C, Staufner C, Storey I, Stormon M, Taylor RW, Thorburn DR, Teles EL, Wang JS, Weghuber D, Wortmann S. Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants. Genet Med 2022:S1098-3600(22)00953-4. [DOI: 10.1016/j.gim.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
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16
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Wong W, Balasubramaniam S, Wong RSH, Graf N, Thorburn DR, McFarland R, Troedson C. Mitochondrial respiratory chain dysfunction in a patient with a heterozygous de novo
CTBP1
variant. JIMD Rep 2022; 63:546-554. [DOI: 10.1002/jmd2.12326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Wui‐Kwan Wong
- TY Nelson Department of Neurology and Neurosurgery The Children's Hospital at Westmead Sydney New South Wales Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Sydney New South Wales Australia
- Discipline of Genomic Medicine, Sydney Medical School University of Sydney Sydney New South Wales Australia
| | - Rachel S. H. Wong
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Sydney New South Wales Australia
| | - Nicole Graf
- Department of Histopathology The Children's Hospital at Westmead Sydney Australia
| | - David R. Thorburn
- Murdoch Children's Research Institute Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Victorian Clinical Genetics Services Melbourne Victoria Australia
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences Newcastle University Newcastle upon Tyne UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders Newcastle upon Tyne Hospitals NHS Foundation Trust Newcastle upon Tyne UK
| | - Christopher Troedson
- TY Nelson Department of Neurology and Neurosurgery The Children's Hospital at Westmead Sydney New South Wales Australia
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17
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Andzelm MM, Balasubramaniam S, Yang E, Compton AG, Millington K, Zhu J, Anselm I, Rodan LH, Thorburn DR, Christodoulou J, Srivastava S. Expansion of the clinical and neuroimaging spectrum associated with NDUFS8-related disorder. JIMD Rep 2022; 63:391-399. [PMID: 36101822 PMCID: PMC9458602 DOI: 10.1002/jmd2.12303] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022] Open
Abstract
Biallelic pathogenic variants in NDUFS8, a nuclear gene encoding a subunit of mitochondrial complex I, result in a mitochondrial disorder characterized by varying clinical presentations and severity. Here, we expand the neuroimaging and clinical spectrum of NDUFS8-related disorder. We present three cases from two unrelated families (a girl and two brothers) homozygous for a recurrent pathogenic NDUFS8 variant [c.460G>A, p.(Gly154Ser)], located in the [4Fe-4S] domain of the protein. One of the patients developed auto-antibody positive diabetic ketoacidosis. Brain MRIs performed in two of the three patients demonstrated diffuse cerebral and cerebellar white matter involvement including corticospinal tracts, but notably had sparing of deep gray matter structures. Our report expands the neuroimaging phenotype of NDUFS8-related disorder to include progressive leukodystrophy with increasing brainstem and cerebellar involvement, with relative sparing of the basal ganglia. In addition, we describe autoimmune diabetes in association with NDUFS8-related disorder, though the exact mechanism of this association is unclear. This paper provides a comprehensive review of case presentation and progressive neuroimaging findings of three patients from two unrelated families that have an identical pathogenic NDUFS8 variant, which expands the clinical spectrum of NDUFS8-associated neurological disease.
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Affiliation(s)
- Milena M. Andzelm
- Department of NeurologyChildren's Hospital BostonBostonMassachusettsUSA
| | - Shanti Balasubramaniam
- Western Sydney Genetics ProgramThe Children's Hospital at WestmeadSydneyNew South WalesAustralia,Department of Metabolic Medicine and RheumatologyPerth Children's HospitalPerthWestern AustraliaAustralia
| | - Edward Yang
- Department of RadiologyChildren's Hospital BostonBostonMassachusettsUSA
| | - Alison G. Compton
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Kate Millington
- Division of Endocrinology, Department of PediatricsChildren's Hospital BostonBostonMassachusettsUSA
| | - Jia Zhu
- Division of Endocrinology, Department of PediatricsChildren's Hospital BostonBostonMassachusettsUSA
| | - Irina Anselm
- Department of NeurologyChildren's Hospital BostonBostonMassachusettsUSA
| | - Lance H. Rodan
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of PediatricsChildren's Hospital BostonBostonMassachusettsUSA
| | - David R. Thorburn
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia,Victorian Clinical Genetic ServicesMelbourneVictoriaAustralia
| | - John Christodoulou
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia,Victorian Clinical Genetic ServicesMelbourneVictoriaAustralia
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18
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Guimier A, Achleitner MT, Moreau de Bellaing A, Edwards M, de Pontual L, Mittal K, Dunn KE, Grove ME, Tysoe CJ, Dimartino C, Cameron J, Kanthi A, Shukla A, van den Broek F, Chatterjee D, Alston CL, Knowles CV, Brett L, Till JA, Homfray T, French P, Spentzou G, Elserafy NA, Lichkus KS, Sankaran BP, Kennedy HL, George PM, Kidd A, Wortmann SB, Fisk DG, Koopmann TT, Rafiq MA, Merker JD, Parikh S, Ahimaz P, Weintraub RG, Ma AS, Turner C, Ellaway CJ, Phillips LK, Thorburn DR, Chung WK, Kana SL, Faye-Petersen OM, Thompson ML, Janin A, McLeod K, McGowan R, McFarland R, Girisha KM, Morris-Rosendahl DJ, Hurst ACE, Turner CLS, Hamilton RM, Taylor RW, Bajolle F, Gordon CT, Amiel J, Mayr JA, Doudney K. PPA2-associated sudden cardiac death: extending the clinical and allelic spectrum in 20 new families. Genet Med 2022; 24:967. [PMID: 35394429 DOI: 10.1016/j.gim.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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19
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Jackson TD, Crameri JJ, Muellner-Wong L, Frazier AE, Palmer CS, Formosa LE, Hock DH, Fujihara KM, Stait T, Sharpe AJ, Thorburn DR, Ryan MT, Stroud DA, Stojanovski D. Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module. Proc Natl Acad Sci U S A 2022; 119:e2115566119. [PMID: 35333655 PMCID: PMC9060475 DOI: 10.1073/pnas.2115566119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/11/2022] [Indexed: 12/23/2022] Open
Abstract
SignificanceMitochondria are double-membraned eukaryotic organelles that house the proteins required for generation of ATP, the energy currency of cells. ATP generation within mitochondria is performed by five multisubunit complexes (complexes I to V), the assembly of which is an intricate process. Mutations in subunits of these complexes, or the suite of proteins that help them assemble, lead to a severe multisystem condition called mitochondrial disease. We show that SFXN4, a protein that causes mitochondrial disease when mutated, assists with the assembly of complex I. This finding explains why mutations in SFXN4 cause mitochondrial disease and is surprising because SFXN4 belongs to a family of amino acid transporter proteins, suggesting that it has undergone a dramatic shift in function through evolution.
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Affiliation(s)
- Thomas D. Jackson
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Ann E. Frazier
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Catherine S. Palmer
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Luke E. Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Daniella H. Hock
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kenji M. Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tegan Stait
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Alice J. Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, 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 3052, Australia
- Victorian Clinical Genetic Services, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Michael T. Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - David A. Stroud
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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20
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Akesson LS, Rius R, Brown NJ, Rosenbaum J, Donoghue S, Stormon M, Chai C, Bordador E, Guo Y, Hakonarson H, Compton AG, Thorburn DR, Amarasekera S, Marum J, Monaco A, Lee C, Chong B, Lunke S, Stark Z, Christodoulou J. Distinct diagnostic trajectories in
NBAS
‐associated acute liver failure highlights the need for timely functional studies. JIMD Rep 2022; 63:240-249. [PMID: 35433172 PMCID: PMC8995841 DOI: 10.1002/jmd2.12280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Variants of uncertain significance (VUS) are commonly found following genomic sequencing, particularly in ethnically diverse populations that are underrepresented in large population databases. Functional characterization of VUS may assist in variant reclassification, however these studies are not readily available and often rely on research funding and good will. We present four individuals from three families at different stages of their diagnostic trajectory with recurrent acute liver failure (RALF) and biallelic NBAS variants, confirmed by either trio analysis or cDNA studies. Functional characterization was undertaken, measuring NBAS and p31 levels by Western blotting, demonstrating reduced NBAS levels in two of three families, and reduced p31 levels in all three families. These results provided functional characterization of the molecular impact of a missense VUS, allowing reclassification of the variant and molecular confirmation of NBAS‐associated RALF. Importantly, p31 was decreased in all individuals, including an individual with two missense variants where NBAS protein levels were preserved. These results highlight the importance of access to timely functional studies after identification of putative variants, and the importance of considering a range of assays to validate variants whose pathogenicity is uncertain. We suggest that funding models for genomic sequencing should consider incorporating capabilities for adjunct RNA, protein, biochemical, and other specialized tests to increase the diagnostic yield which will lead to improved medical care, increased equity, and access to molecular diagnoses for all patients.
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Affiliation(s)
- Lauren S. Akesson
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- SA Pathology SA Health Adelaide SA Australia
- School of Biomedicine, Faculty of Medicine, Dentistry and Health Sciences University of Adelaide Adelaide Australia Australia
| | - Rocio Rius
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Brain and Mitochondrial Research Group Murdoch Children's Research Institute, Royal Children's Hospital Melbourne Victoria Australia
| | - Natasha J. Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
| | - Jeremy Rosenbaum
- Department of Gastroenterology Royal Children's Hospital Melbourne Victoria Australia
| | - Sarah Donoghue
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Metabolic Medicine Royal Children's Hospital Melbourne Victoria Australia
| | - Michael Stormon
- Department of Gastroenterology Children's Hospital Westmead Sydney New South Wales Australia
- Discipline of Child & Adolescent Health, Sydney Medical School University of Sydney Sydney New South Wales Australia
| | - Charmaine Chai
- Department of Gastroenterology Children's Hospital Westmead Sydney New South Wales Australia
| | - Esmeralda Bordador
- Department of Metabolic Medicine Royal Children's Hospital Melbourne Victoria Australia
| | - Yiran Guo
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Center for Data‐Driven Discovery in Biomedicine Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Hakon Hakonarson
- Center for Applied Genomics Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Pediatrics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Alison G. Compton
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Brain and Mitochondrial Research Group Murdoch Children's Research Institute, Royal Children's Hospital Melbourne Victoria Australia
| | - David R. Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Brain and Mitochondrial Research Group Murdoch Children's Research Institute, Royal Children's Hospital Melbourne Victoria Australia
| | - Sumudu Amarasekera
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Brain and Mitochondrial Research Group Murdoch Children's Research Institute, Royal Children's Hospital Melbourne Victoria Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Alisha Monaco
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Crystle Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Pathology University of Melbourne Melbourne Victoria Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Brain and Mitochondrial Research Group Murdoch Children's Research Institute, Royal Children's Hospital Melbourne Victoria Australia
- Discipline of Child & Adolescent Health, Sydney Medical School University of Sydney Sydney New South Wales Australia
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21
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Lee RG, Balasubramaniam S, Stentenbach M, Kralj T, McCubbin T, Padman B, Smith J, Riley LG, Priyadarshi A, Peng L, Nuske MR, Webster R, Peacock K, Roberts P, Stark Z, Lemire G, Ito YA, Boycott KM, Geraghty MT, van Klinken JB, Ferdinandusse S, Zhou Y, Walsh R, Marcellin E, Thorburn DR, Rosciolli T, Fletcher J, Rackham O, Vaz FM, Reid GE, Filipovska A. Deleterious variants in CRLS1 lead to cardiolipin deficiency and cause an autosomal recessive multi-system mitochondrial disease. Hum Mol Genet 2022; 31:3597-3612. [PMID: 35147173 PMCID: PMC9616573 DOI: 10.1093/hmg/ddac040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial diseases are a group of inherited diseases with highly varied and complex clinical presentations. Here, we report four individuals, including two siblings, affected by a progressive mitochondrial encephalopathy with biallelic variants in the cardiolipin biosynthesis gene CRLS1. Three affected individuals had a similar infantile presentation comprising progressive encephalopathy, bull's eye maculopathy, auditory neuropathy, diabetes insipidus, autonomic instability, cardiac defects and early death. The fourth affected individual presented with chronic encephalopathy with neurodevelopmental regression, congenital nystagmus with decreased vision, sensorineural hearing loss, failure to thrive and acquired microcephaly. Using patient-derived fibroblasts, we characterized cardiolipin synthase 1 (CRLS1) dysfunction that impaired mitochondrial morphology and biogenesis, providing functional evidence that the CRLS1 variants cause mitochondrial disease. Lipid profiling in fibroblasts from two patients further confirmed the functional defect demonstrating reduced cardiolipin levels, altered acyl-chain composition and significantly increased levels of phosphatidylglycerol, the substrate of CRLS1. Proteomic profiling of patient cells and mouse Crls1 knockout cell lines identified both endoplasmic reticular and mitochondrial stress responses, and key features that distinguish between varying degrees of cardiolipin insufficiency. These findings support that deleterious variants in CRLS1 cause an autosomal recessive mitochondrial disease, presenting as a severe encephalopathy with multi-systemic involvement. Furthermore, we identify key signatures in cardiolipin and proteome profiles across various degrees of cardiolipin loss, facilitating the use of omics technologies to guide future diagnosis of mitochondrial diseases.
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Affiliation(s)
| | | | - Maike Stentenbach
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA 6009, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia,ARC Centre of Excellence in Synthetic Biology, Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Tom Kralj
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, and Queensland Node of Metabolomics Australia,The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin Padman
- Centre for Microscopy, Characterisation and Analysis, The University of WA, Perth, WA 6009, Australia
| | - Janine Smith
- Discipline of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia,Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children’s Hospital at Westmead and Children’s Medical Research Institute, Sydney, NSW 2145, Australia,Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2145, Australia
| | - Archana Priyadarshi
- Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2145, Australia,Neonatal Intensive Care Unit, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Liuyu Peng
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Madison R Nuske
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Richard Webster
- Department of Paediatrics, University of Melbourne, VIC 3052, Australia
| | - Ken Peacock
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,General Paediatric Medicine, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Philip Roberts
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Zornitza Stark
- University of Melbourne, Parkville, VIC 3052, Australia,Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia
| | - Gabrielle Lemire
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Yoko A Ito
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | - Kym M Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Michael T Geraghty
- Metabolics and Newborn Screening, Pediatrics, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Jan Bert van Klinken
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands,Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands,Department of Human Genetics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Sacha Ferdinandusse
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Ying Zhou
- NSW Health Pathology, Randwick, NSW 2145, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, and Queensland Node of Metabolomics Australia,The University of Queensland, St Lucia, QLD 4072, Australia
| | - David R Thorburn
- University of Melbourne, Parkville, VIC 3052, Australia,Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Tony Rosciolli
- NSW Health Pathology, Randwick, NSW 2145, Australia,Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, NSW 2145, Australia
| | | | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA 6009, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia,ARC Centre of Excellence in Synthetic Biology, Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia,Curtin Medical School, Curtin University, Bentley, WA 6102, Australia,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Frédéric M Vaz
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands,Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands,Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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22
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Van Bergen NJ, Hock DH, Spencer L, Massey S, Stait T, Stark Z, Lunke S, Roesley A, Peters H, Lee JY, Le Fevre A, Heath O, Mignone C, Yang JYM, Ryan MM, D’Arcy C, Nash M, Smith S, Caruana NJ, Thorburn DR, Stroud DA, White SM, Christodoulou J, Brown NJ. Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. Int J Mol Sci 2022; 23:ijms23020986. [PMID: 35055180 PMCID: PMC8777681 DOI: 10.3390/ijms23020986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/04/2022] Open
Abstract
Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein’s precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child’s clinical presentation.
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Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Daniella H. Hock
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Lucy Spencer
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Tegan Stait
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
| | - Sebastian Lunke
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Heidi Peters
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Joy Yaplito Lee
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Oliver Heath
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Cristina Mignone
- Medical Imaging Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Joseph Yuan-Mou Yang
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Neurosurgery, Neuroscience Advanced Clinical Imaging Service (NACIS), The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Developmental Imaging, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Neuroscience Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Monique M. Ryan
- Neurology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Colleen D’Arcy
- Anatomical Pathology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Margot Nash
- General Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Sile Smith
- Paediatric Intensive Care Unit, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Nikeisha J. Caruana
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC 3011, Australia
| | - David R. Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - David A. Stroud
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Discipline of Child and Adolescent Health, University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Natasha J. Brown
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
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23
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Granata C, Caruana NJ, Botella J, Jamnick NA, Huynh K, Kuang J, Janssen HA, Reljic B, Mellett NA, Laskowski A, Stait TL, Frazier AE, Coughlan MT, Meikle PJ, Thorburn DR, Stroud DA, Bishop DJ. High-intensity training induces non-stoichiometric changes in the mitochondrial proteome of human skeletal muscle without reorganisation of respiratory chain content. Nat Commun 2021; 12:7056. [PMID: 34862379 PMCID: PMC8642543 DOI: 10.1038/s41467-021-27153-3] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial defects are implicated in multiple diseases and aging. Exercise training is an accessible, inexpensive therapeutic intervention that can improve mitochondrial bioenergetics and quality of life. By combining multiple omics techniques with biochemical and in silico normalisation, we removed the bias arising from the training-induced increase in mitochondrial content to unearth an intricate and previously undemonstrated network of differentially prioritised mitochondrial adaptations. We show that changes in hundreds of transcripts, proteins, and lipids are not stoichiometrically linked to the overall increase in mitochondrial content. Our findings suggest enhancing electron flow to oxidative phosphorylation (OXPHOS) is more important to improve ATP generation than increasing the abundance of the OXPHOS machinery, and do not support the hypothesis that training-induced supercomplex formation enhances mitochondrial bioenergetics. Our study provides an analytical approach allowing unbiased and in-depth investigations of training-induced mitochondrial adaptations, challenging our current understanding, and calling for careful reinterpretation of previous findings.
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Affiliation(s)
- Cesare Granata
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia.
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Nikeisha J Caruana
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Javier Botella
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Nicholas A Jamnick
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
- Metabolic Research Unit, School of Medicine and Institute for Mental and Physical Health and Clinical Translation (iMPACT), Deakin University, Geelong, VIC, Australia
| | - Kevin Huynh
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Jujiao Kuang
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Hans A Janssen
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Boris Reljic
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | | | - Adrienne Laskowski
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Tegan L Stait
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Peter J Meikle
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
| | - David J Bishop
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia.
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24
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Cloney T, Gallacher L, Pais LS, Tan NB, Yeung A, Stark Z, Brown NJ, McGillivray G, Delatycki MB, de Silva MG, Downie L, Stutterd CA, Elliott J, Compton AG, Lovgren A, Oertel R, Francis D, Bell KM, Sadedin S, Lim SC, Helman G, Simons C, Macarthur DG, Thorburn DR, O'Donnell-Luria AH, Christodoulou J, White SM, Tan TY. Lessons learnt from multifaceted diagnostic approaches to the first 150 families in Victoria's Undiagnosed Diseases Program. J Med Genet 2021; 59:748-758. [PMID: 34740920 DOI: 10.1136/jmedgenet-2021-107902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/02/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Clinical exome sequencing typically achieves diagnostic yields of 30%-57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals. AIM We share the lessons learnt from the first 3 years of the Undiagnosed Diseases Program-Victoria, an Australian programme embedded within a clinical genetics service in the state of Victoria with a focus on paediatric rare diseases. METHODS We enrolled families who remained without a diagnosis after clinical genomic (panel, exome or genome) sequencing between 2016 and 2018. We used family-based exome sequencing (family ES), family-based genome sequencing (family GS), RNA sequencing (RNA-seq) and high-resolution chromosomal microarray (CMA) with research-based analysis. RESULTS In 150 families, we achieved a diagnosis or strong candidate in 64 (42.7%) (37 in known genes with a consistent phenotype, 3 in known genes with a novel phenotype and 24 in novel disease genes). Fifty-four diagnoses or strong candidates were made by family ES, six by family GS with RNA-seq, two by high-resolution CMA and two by data reanalysis. CONCLUSION We share our lessons learnt from the programme. Flexible implementation of multiple strategies allowed for scalability and response to the availability of new technologies. Broad implementation of family ES with research-based analysis showed promising yields post a negative clinical singleton ES. RNA-seq offered multiple benefits in family ES-negative populations. International data sharing strategies were critical in facilitating collaborations to establish novel disease-gene associations. Finally, the integrated approach of a multiskilled, multidisciplinary team was fundamental to having diverse perspectives and strategic decision-making.
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Affiliation(s)
- Thomas Cloney
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lynn S Pais
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lilian Downie
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alysia Lovgren
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Analytic and Translational Genomics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ralph Oertel
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sze Chern Lim
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Guy Helman
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Translational Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Daniel G Macarthur
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anne H O'Donnell-Luria
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Neurodevelopmental Genomics Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia .,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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25
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Ng YS, Bindoff LA, Gorman GS, Klopstock T, Kornblum C, Mancuso M, McFarland R, Sue CM, Suomalainen A, Taylor RW, Thorburn DR, Turnbull DM. Mitochondrial disease in adults: recent advances and future promise. Lancet Neurol 2021; 20:573-584. [PMID: 34146515 DOI: 10.1016/s1474-4422(21)00098-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Mitochondrial diseases are some of the most common inherited neurometabolic disorders, and major progress has been made in our understanding, diagnosis, and treatment of these conditions in the past 5 years. Development of national mitochondrial disease cohorts and international collaborations has changed our knowledge of the spectrum of clinical phenotypes and natural history of mitochondrial diseases. Advances in high-throughput sequencing technologies have altered the diagnostic algorithm for mitochondrial diseases by increasingly using a genetics-first approach, with more than 350 disease-causing genes identified to date. While the current management strategy for mitochondrial disease focuses on surveillance for multisystem involvement and effective symptomatic treatment, new endeavours are underway to find better treatments, including repurposing current drugs, use of novel small molecules, and gene therapies. Developments made in reproductive technology offer women the opportunity to prevent transmission of DNA-related mitochondrial disease to their children.
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Affiliation(s)
- Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Directorate of Neurosciences, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Laurence A Bindoff
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Directorate of Neurosciences, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, LMU Hospital, Ludwig Maximilians University, Munich, Germany; German Center for Neurodegenerative Diseases, Munich, Germany; Munich Cluster for Systems Neurology, Munich, Germany
| | - Cornelia Kornblum
- Department of Neurology, Neuromuscular Disease Section, University Hospital Bonn, Bonn, Germany; Centre for Rare Diseases, University Hospital Bonn, Bonn, Germany
| | - Michelangelo Mancuso
- Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, Italy
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, St Leonards, NSW, Australia
| | - Anu Suomalainen
- Research Program in Stem Cells and Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Neuroscience Centre, HiLife, University of Helsinki, Helsinki, Finland; Helsinki University Hospital, HUSlab, Helsinki, Finland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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26
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McKnight CL, Low YC, Elliott DA, Thorburn DR, Frazier AE. Modelling Mitochondrial Disease in Human Pluripotent Stem Cells: What Have We Learned? Int J Mol Sci 2021; 22:7730. [PMID: 34299348 PMCID: PMC8306397 DOI: 10.3390/ijms22147730] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial diseases disrupt cellular energy production and are among the most complex group of inherited genetic disorders. Affecting approximately 1 in 5000 live births, they are both clinically and genetically heterogeneous, and can be highly tissue specific, but most often affect cell types with high energy demands in the brain, heart, and kidneys. There are currently no clinically validated treatment options available, despite several agents showing therapeutic promise. However, modelling these disorders is challenging as many non-human models of mitochondrial disease do not completely recapitulate human phenotypes for known disease genes. Additionally, access to disease-relevant cell or tissue types from patients is often limited. To overcome these difficulties, many groups have turned to human pluripotent stem cells (hPSCs) to model mitochondrial disease for both nuclear-DNA (nDNA) and mitochondrial-DNA (mtDNA) contexts. Leveraging the capacity of hPSCs to differentiate into clinically relevant cell types, these models permit both detailed investigation of cellular pathomechanisms and validation of promising treatment options. Here we catalogue hPSC models of mitochondrial disease that have been generated to date, summarise approaches and key outcomes of phenotypic profiling using these models, and discuss key criteria to guide future investigations using hPSC models of mitochondrial disease.
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Affiliation(s)
- Cameron L. McKnight
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (C.L.M.); (Y.C.L.); (D.A.E.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yau Chung Low
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (C.L.M.); (Y.C.L.); (D.A.E.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - David A. Elliott
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (C.L.M.); (Y.C.L.); (D.A.E.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (C.L.M.); (Y.C.L.); (D.A.E.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Parkville, VIC 3052, Australia
| | - Ann E. Frazier
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (C.L.M.); (Y.C.L.); (D.A.E.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
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27
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Wu Y, Balasubramaniam S, Rius R, Thorburn DR, Christodoulou J, Goranitis I. Genomic sequencing for the diagnosis of childhood mitochondrial disorders: a health economic evaluation. Eur J Hum Genet 2021; 30:577-586. [PMID: 34099885 PMCID: PMC9090793 DOI: 10.1038/s41431-021-00916-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022] Open
Abstract
The diagnostic and clinical benefits of genomic sequencing are being increasingly demonstrated across multiple rare genetic conditions. Despite the expanding clinical literature, there is a significant paucity of health economics evidence to inform the prioritization and implementation of genomic sequencing. This study aims to evaluate whether genomic sequencing for pediatric-onset mitochondrial disorders (MDs) is cost-effective and cost-beneficial relative to conventional care from an Australian healthcare system perspective. Two independent and complementary health economic modeling approaches were used. Approach 1 used a decision tree to model the costs and outcomes associated with genomic sequencing and conventional care. Approach 2 used a discrete-event simulation to incorporate heterogeneity in the condition and clinical practice. Deterministic and probabilistic sensitivity analyses were performed. Genomic sequencing was less costly and more effective compared with conventional care, saving AU$1997 (Approach 1) to AU$8823 (Approach 2) per child tested, while leading to an additional 11 (Approach 1) to 14 (Approach 2) definitive diagnoses per 100 children tested. The mean monetary value of the incremental benefits of genomic sequencing was estimated at AU$5890 (95% CI: AU$5730-$6046). Implementation of genomic sequencing for MDs in Australia could translate to an annual cost-saving of up to AU$0.7 million. Genomic sequencing is cost-saving relative to traditional investigative approaches, while enabling more diagnoses to be made in a timely manner, offering substantial personal benefits to children and their families. Our findings support the prioritization of genomic sequencing for children with MDs.
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Affiliation(s)
- You Wu
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - David R Thorburn
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, Australia
| | - John Christodoulou
- Australian Genomics Health Alliance, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia. .,Australian Genomics Health Alliance, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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28
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Rius R, Compton AG, Baker NL, Welch AE, Coman D, Kava MP, Minoche AE, Cowley MJ, Thorburn DR, Christodoulou J. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. Genes (Basel) 2021; 12:genes12040607. [PMID: 33924034 PMCID: PMC8072654 DOI: 10.3390/genes12040607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related costs and challenges in data analysis. In this article, we report three patients with mitochondrial disease molecularly diagnosed through GS performed on DNA extracted from blood to demonstrate different diagnostic advantages of this technology, including the detection of a low-level heteroplasmic pathogenic variant, an intragenic nuclear DNA deletion, and a large mtDNA deletion. Current technical improvements and cost reductions are likely to lead to an expanded routine diagnostic usage of GS and of the complementary “Omic” technologies in mitochondrial diseases.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Naomi L. Baker
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - AnneMarie E. Welch
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
| | - David Coman
- Department of Metabolic Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia;
- School of Clinical Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- School of Medicine, Griffith University, Gold Coast, QLD 4222, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia;
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +61-39936-6353
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29
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Barcia G, Pandithan D, Ruzzenente B, Assouline Z, Pennisi A, Ormieres C, Besmond C, Roux CJ, Boddaert N, Desguerre I, Thorburn DR, Bratkovic D, Munnich A, Bonnefont JP, Rötig A, Steffann J. Biallelic <i>IARS2</i> mutations presenting as sideroblastic anemia. Haematologica 2021; 106:1220-1225. [PMID: 33327715 PMCID: PMC8018106 DOI: 10.3324/haematol.2020.270710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 11/09/2022] Open
Abstract
Not available.
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Affiliation(s)
- Giulia Barcia
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris.
| | | | - Benedetta Ruzzenente
- Laboratory for Genetics of Mitochondrial Disorders, UMR 1163, Université de Paris, Institut Imagine, Paris
| | - Zahra Assouline
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris
| | - Alessandra Pennisi
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris
| | - Clothilde Ormieres
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris
| | - Claude Besmond
- Translational Genetics Laboratory, UMR U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris
| | - Charles-Joris Roux
- Department of Pediatric Radiology, Hospital Necker Enfants Malades, Paris
| | - Nathalie Boddaert
- Department of Pediatric Radiology, Hospital Necker Enfants Malades, Paris
| | - Isabelle Desguerre
- Department of Pediatric Neurology, Hospital Necker-Enfants Malades, Paris
| | - David R Thorburn
- Murdoch Children's Research Institute and Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052
| | - Drago Bratkovic
- Metabolic Clinic, Women's and Children's Hospital, North Adelaide
| | - Arnold Munnich
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris, France; Metabolic Clinic, Women's and Children's Hospital, North Adelaide, South Australia; Laboratory for Genetics of Mitochondrial Disorders, UMR 1163, Université de Paris, Institut Imagine, Paris
| | - Jean-Paul Bonnefont
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris, France; Metabolic Clinic, Women's and Children's Hospital, North Adelaide, South Australia; Laboratory for Genetics of Mitochondrial Disorders, UMR 1163, Université de Paris, Institut Imagine, Paris
| | - Agnès Rötig
- Laboratory for Genetics of Mitochondrial Disorders, UMR 1163, Université de Paris, Institut Imagine, Paris
| | - Julie Steffann
- Federation of Medical Genetics and Reference Center for Mitochondrial Diseases (CARAMMEL), Hospital Necker - Enfants Malades, Paris, France; Metabolic Clinic, Women's and Children's Hospital, North Adelaide, South Australia; Laboratory for Genetics of Mitochondrial Disorders, UMR 1163, Université de Paris, Institut Imagine, Paris
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30
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Jackson TD, Hock DH, Fujihara KM, Palmer CS, Frazier AE, Low YC, Kang Y, Ang CS, Clemons NJ, Thorburn DR, Stroud DA, Stojanovski D. The TIM22 complex mediates the import of sideroflexins and is required for efficient mitochondrial one-carbon metabolism. Mol Biol Cell 2021; 32:475-491. [PMID: 33476211 PMCID: PMC8101445 DOI: 10.1091/mbc.e20-06-0390] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Acylglycerol kinase (AGK) is a mitochondrial lipid kinase that contributes to protein biogenesis as a subunit of the TIM22 complex at the inner mitochondrial membrane. Mutations in AGK cause Sengers syndrome, an autosomal recessive condition characterized by congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy, and lactic acidosis. We mapped the proteomic changes in Sengers patient fibroblasts and AGKKO cell lines to understand the effects of AGK dysfunction on mitochondria. This uncovered down-regulation of a number of proteins at the inner mitochondrial membrane, including many SLC25 carrier family proteins, which are predicted substrates of the complex. We also observed down-regulation of SFXN proteins, which contain five transmembrane domains, and show that they represent a novel class of TIM22 complex substrate. Perturbed biogenesis of SFXN proteins in cells lacking AGK reduces the proliferative capabilities of these cells in the absence of exogenous serine, suggesting that dysregulation of one-carbon metabolism is a molecular feature in the biology of Sengers syndrome.
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Affiliation(s)
- Thomas D Jackson
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
| | - Kenji M Fujihara
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3010, Australia.,Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Catherine S Palmer
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
| | - Ann E Frazier
- Murdoch Children's Research Institute and.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Yau C Low
- Murdoch Children's Research Institute and.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Yilin Kang
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas J Clemons
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3010, Australia.,Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute and.,Victorian Clinical Genetics Services Royal Children's Hospital, Melbourne, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute
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31
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Helman G, Compton AG, Hock DH, Walkiewicz M, Brett GR, Pais L, Tan TY, De Paoli-Iseppi R, Clark MB, Christodoulou J, White SM, Thorburn DR, Stroud DA, Stark Z, Simons C. Multiomic analysis elucidates Complex I deficiency caused by a deep intronic variant in NDUFB10. Hum Mutat 2021; 42:19-24. [PMID: 33169436 PMCID: PMC7902361 DOI: 10.1002/humu.24135] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 07/16/2020] [Revised: 09/06/2020] [Accepted: 10/28/2020] [Indexed: 01/01/2023]
Abstract
The diagnosis of Mendelian disorders following uninformative exome and genome sequencing remains a challenging and often unmet need. Following uninformative exome and genome sequencing of a family quartet including two siblings with suspected mitochondrial disorder, RNA sequencing (RNAseq) was pursued in one sibling. Long-read amplicon sequencing was used to determine and quantify transcript structure. Immunoblotting studies and quantitative proteomics were performed to demonstrate functional impact. Differential expression analysis of RNAseq data identified significantly decreased expression of the mitochondrial OXPHOS Complex I subunit NDUFB10 associated with a cryptic exon in intron 1 of NDUFB10, that included an in-frame stop codon. The cryptic exon contained a rare intronic variant that was homozygous in both affected siblings. Immunoblot and quantitative proteomic analysis of fibroblasts revealed decreased abundance of Complex I subunits, providing evidence of isolated Complex I deficiency. Through multiomic analysis we present data implicating a deep intronic variant in NDUFB10 as the cause of mitochondrial disease in two individuals, providing further support of the gene-disease association. This study highlights the importance of transcriptomic and proteomic analyses as complementary diagnostic tools in patients undergoing genome-wide diagnostic evaluation.
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Affiliation(s)
- Guy Helman
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Institute for Molecular Bioscience, The University of Queensland, Queensland, 4072, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Daniella H. Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, 3052, Australia
| | - Marzena Walkiewicz
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - Gemma R. Brett
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA
| | - Tiong Y. Tan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, 3052, Australia
| | - Michael B. Clark
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - David A. Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, 3052, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
| | - Cas Simons
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, 3052, Australia
- Institute for Molecular Bioscience, The University of Queensland, Queensland, 4072, Australia
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32
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Wintjes LTM, Kava M, van den Brandt FA, van den Brand MAM, Lapina O, Bliksrud YT, Kulseth MA, Amundsen SS, Selberg TR, Ybema-Antoine M, Tutakhel OAZ, Greed L, Thorburn DR, Tangeraas T, Balasubramaniam S, Rodenburg RJT. A novel variant in COX16 causes cytochrome c oxidase deficiency, severe fatal neonatal lactic acidosis, encephalopathy, cardiomyopathy, and liver dysfunction. Hum Mutat 2020; 42:135-141. [PMID: 33169484 PMCID: PMC7898715 DOI: 10.1002/humu.24137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Received: 07/16/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 01/28/2023]
Abstract
COX16 is involved in the biogenesis of cytochrome-c-oxidase (complex IV), the terminal complex of the mitochondrial respiratory chain. We present the first report of two unrelated patients with the homozygous nonsense variant c.244C>T(p. Arg82*) in COX16 with hypertrophic cardiomyopathy, encephalopathy and severe fatal lactic acidosis, and isolated complex IV deficiency. The absence of COX16 protein expression leads to a complete loss of the holo-complex IV, as detected by Western blot in patient fibroblasts. Lentiviral transduction of patient fibroblasts with wild-type COX16 complementary DNA rescued complex IV biosynthesis. We hypothesize that COX16 could play a role in the copper delivery route of the COX2 module as part of the complex IV assembly. Our data provide clear evidence for the pathogenicity of the COX16 variant as a cause for the observed clinical features and the isolated complex IV deficiency in these two patients and that COX16 deficiency is a cause for mitochondrial disease.
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Affiliation(s)
- Liesbeth T M Wintjes
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Maina Kava
- Department of Neurology, Perth Children's Hospital, Perth, Western Australia, Australia.,School of Pediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Frans A van den Brandt
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Mariël A M van den Brand
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Oksana Lapina
- Department for Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Yngve T Bliksrud
- Norwegian National Unit for Diagnostics of Congenital Metabolic Disorders, Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Mari A Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Silja S Amundsen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Terje R Selberg
- Department of Pediatrics, Ostfold Hospital Trust, Kalnes, Norway
| | - Marion Ybema-Antoine
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Omar A Z Tutakhel
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Lawrence Greed
- Department of Clinical Biochemistry, PathWest, Perth, Western Australia, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute and Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Trine Tangeraas
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Shanti Balasubramaniam
- Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Richard J T Rodenburg
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands.,Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
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33
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Riley LG, Rudinger-Thirion J, Frugier M, Wilson M, Luig M, Alahakoon TI, Nixon CY, Kirk EP, Roscioli T, Lunke S, Stark Z, Wierenga KJ, Palle S, Walsh M, Higgs E, Arbuckle S, Thirukeswaran S, Compton AG, Thorburn DR, Christodoulou J. The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy. Hum Mutat 2020; 41:1425-1434. [PMID: 32442335 DOI: 10.1002/humu.24050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 01/24/2020] [Revised: 04/22/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022]
Abstract
LARS2 variants are associated with Perrault syndrome, characterized by premature ovarian failure and hearing loss, and with an infantile lethal multisystem disorder: Hydrops, lactic acidosis, sideroblastic anemia (HLASA) in one individual. Recently we reported LARS2 deafness with (ovario) leukodystrophy. Here we describe five patients with a range of phenotypes, in whom we identified biallelic LARS2 variants: three patients with a HLASA-like phenotype, an individual with Perrault syndrome whose affected siblings also had leukodystrophy, and an individual with a reversible mitochondrial myopathy, lactic acidosis, and developmental delay. Three HLASA cases from two unrelated families were identified. All were males with genital anomalies. Two survived multisystem disease in the neonatal period; both have developmental delay and hearing loss. A 55-year old male with deafness has not displayed neurological symptoms while his female siblings with Perrault syndrome developed leukodystrophy and died in their 30s. Analysis of muscle from a child with a reversible myopathy showed reduced LARS2 and mitochondrial complex I levels, and an unusual form of degeneration. Analysis of recombinant LARS2 variant proteins showed they had reduced aminoacylation efficiency, with HLASA-associated variants having the most severe effect. A broad phenotypic spectrum should be considered in association with LARS2 variants.
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Affiliation(s)
- Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, Australia.,Discipline of Child & Adolescent Health, Sydney Medical School, Sydney, Australia
| | - Joëlle Rudinger-Thirion
- Université de Strasbourg, Architecture et Réactivité de l'ARN, CNRS, IBMC, Strasbourg, France
| | - Magali Frugier
- Université de Strasbourg, Architecture et Réactivité de l'ARN, CNRS, IBMC, Strasbourg, France
| | - Meredith Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, Australia.,Discipline of Genomic Medicine, University of Sydney, Sydney, Australia
| | - Melissa Luig
- Department of Neonatology, Westmead Hospital, Sydney, Australia
| | - Thushari Indika Alahakoon
- Westmead Institute for Maternal & Fetal Medicine, Westmead Hospital & University of Sydney, Sydney, Australia
| | - Cheng Yee Nixon
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia.,Genetics Laboratory, NSW Health Pathology, Sydney, Australia
| | - Edwin P Kirk
- Genetics Laboratory, NSW Health Pathology, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, The Royal Children's Hospital, Melbourne, Australia.,Department of Pathology, University of Melbourne, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, The Royal Children's Hospital, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Klaas J Wierenga
- Department of Pediatrics, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK.,Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Sirish Palle
- Department of Pediatrics, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK
| | - Maie Walsh
- Genetic Medicine & Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, Australia
| | - Emily Higgs
- Genetic Medicine & Familial Cancer Centre, Royal Melbourne Hospital, Melbourne, Australia
| | - Susan Arbuckle
- Department of Pathology, The Children's Hospital at Westmead, Sydney, Australia
| | - Shalini Thirukeswaran
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Alison G Compton
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, The Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - John Christodoulou
- Discipline of Child & Adolescent Health, Sydney Medical School, Sydney, Australia.,Victorian Clinical Genetics Services, The Royal Children's Hospital, Melbourne, Australia.,Australian Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
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34
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Newson AJ, de Lacey S, Dowling DK, Murray S, Sue CM, Thorburn DR, Gillam L, Degeling C. Public attitudes towards novel reproductive technologies: a citizens' jury on mitochondrial donation. Hum Reprod 2020; 34:751-757. [PMID: 30865256 PMCID: PMC6443113 DOI: 10.1093/humrep/dez021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 01/11/2019] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION Does an informed group of citizens endorse the clinical use of mitochondrial donation in a country where this is not currently permitted? SUMMARY ANSWER After hearing balanced expert evidence and having opportunity for deliberation, a majority (11/14) of participants in a citizens’ jury believed that children should be able to be born using mitochondrial donation. WHAT IS KNOWN ALREADY Research suggests that patients, oocyte donors and health professionals support mitochondrial donation to prevent transmission of mitochondrial disease. Less is known about public acceptability of this novel reproductive technology, especially from evidence using deliberative methods. STUDY DESIGN, SIZE, DURATION This study comprised a citizens’ jury, an established method for determining the views of a well-informed group of community members. The jury had 14 participants, and ran over one and a half days in 2017. PARTICIPANTS/MATERIALS, SETTING, METHODS Jurors were members of the public with no experience of mitochondrial disease. They heard and engaged with relevant evidence and were asked to answer the question: ‘Should Australia allow children to be born following mitochondrial donation?’ MAIN RESULTS AND THE ROLE OF CHANCE Eleven jurors decided that Australia should allow children to be born following mitochondrial donation; 7 of whom added conditions such as the need to limit who can access the intervention. Three jurors decided that children should not (or not yet) be born using this intervention. All jurors were particularly interested in the reliability of evidence, licensing/regulatory mechanisms and the rights of children to access information about their oocyte donors. LIMITATIONS, REASONS FOR CAUTION Jurors’ views were well informed and reflected critical deliberation and discussion, but are not intended to be representative of the whole population. WIDER IMPLICATIONS OF THE FINDINGS When presented with high quality evidence, combined with opportunities to undertake structured deliberation of novel reproductive technologies, members of the public are able to engage in detailed discussions. This is the first study to use an established deliberative method to gauge public views towards mitochondrial donation. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by a University of Sydney Industry and Community Collaboration Seed Award (2017), which was awarded contingent on additional funding from the Mito Foundation. Additional funding was provided by the Mito Foundation. The Foundation was not involved in jury facilitation or deliberation, nor analysis of research data. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- A J Newson
- The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, Sydney, New South Wales, Australia
| | - S de Lacey
- College of Nursing & Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - D K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - S Murray
- Mito Foundation, Surry Hills, New South Wales, Australia
| | - C M Sue
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St. Leonards, Sydney, Australia.,The University of Sydney, Faculty of Medicine and Health, Sydney Medical School-Northern, Sydney, New South Wales, Australia.,Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, New South Wales, Australia
| | - D R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - L Gillam
- Children's Bioethics Centre, Royal Children's Hospital, Melbourne, Victoria, Australia.,School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - C Degeling
- Australian Centre for Health Engagement, Evidence and Values, Faculty of Social Science, University of Wollongong, Wollongong, New South Wales, Australia
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35
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Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M, Lake NJ, Tregoning S, Jabbari JS, Lucattini A, Nitta KR, Ohtake A, Murayama K, Amor DJ, McGillivray G, Wong FY, van der Knaap MS, Jeroen Vermeulen R, Wiltshire EJ, Fletcher JM, Lewis B, Baynam G, Ellaway C, Balasubramaniam S, Bhattacharya K, Freckmann ML, Arbuckle S, Rodriguez M, Taft RJ, Sadedin S, Cowley MJ, Minoche AE, Calvo SE, Mootha VK, Ryan MT, Okazaki Y, Stroud DA, Simons C, Christodoulou J, Thorburn DR. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. Med (N Y) 2020; 2:49-73. [PMID: 33575671 DOI: 10.1016/j.medj.2020.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.
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Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Alison G Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Daniella H Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - AnneMarie E Welch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - 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 3052, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.,Division of Genomic Medicine Research, Medical Genomics Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Min Wang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nicole J Lake
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Simone Tregoning
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University Hospital, Saitama, 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flora Y Wong
- Ritchie Centre, Hudson Institute of Medical Research; Department of Paediatrics, Monash University; and Monash Newborn, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Marjo S van der Knaap
- Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands
| | - R Jeroen Vermeulen
- Department of Neurology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | - Esko J Wiltshire
- Department of Paediatrics and Child Health, University of Otago Wellington and Capital and Coast District Health Board, Wellington 6021, New Zealand
| | - Janice M Fletcher
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Barry Lewis
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and King Edward Memorial Hospital for Women Perth, Subiaco, WA 6008, Australia.,Telethon Kids Institute and School of Paediatrics and Child Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | | | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW 2145, Australia
| | - Michael Rodriguez
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Simon Sadedin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Kensington, NSW 2750, Australia; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - 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; Harvard Medical School, Boston, MA 02446, USA
| | - 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; Harvard Medical School, Boston, MA 02446, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, 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 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Lead contact
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Hock DH, Reljic B, Ang CS, Muellner-Wong L, Mountford HS, Compton AG, Ryan MT, Thorburn DR, Stroud DA. HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV. Mol Cell Proteomics 2020; 19:1145-1160. [PMID: 32317297 PMCID: PMC7338084 DOI: 10.1074/mcp.ra120.002076] [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: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Assembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. Several assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. Although in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.
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Affiliation(s)
- Daniella H Hock
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Boris Reljic
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Hayley S Mountford
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Alison G Compton
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia; Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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Kang Y, Anderson AJ, Jackson TD, Palmer CS, De Souza DP, Fujihara KM, Stait T, Frazier AE, Clemons NJ, Tull D, Thorburn DR, McConville MJ, Ryan MT, Stroud DA, Stojanovski D. Correction: Function of hTim8a in complex IV assembly in neuronal cells provides insight into pathomechanism underlying Mohr-Tranebjærg syndrome. eLife 2020; 9:56968. [PMID: 32186514 PMCID: PMC7080502 DOI: 10.7554/elife.56968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Measurement of the individual enzymes involved in mitochondrial oxidative phosphorylation (OXPHOS) forms a key part of diagnostic investigations in patients with suspected mitochondrial disease, and can provide crucial information on mitochondrial OXPHOS function in a variety of cells and tissues that are applicable to many research investigations. In this chapter, we present methods for analysis of mitochondrial respiratory chain enzymes in cells and tissues based on assays performed in two geographically separate diagnostic referral centers, as part of clinical diagnostic investigations. Techniques for sample preparation from cells and tissues, and spectrophotometric assays for measurement of the activities of OXPHOS complexes I-V, the combined activity of complexes II+III, and the mitochondrial matrix enzyme citrate synthase, are provided. The activities of mitochondrial respiratory chain enzymes are often expressed relative to citrate synthase activity, since these ratios may be more robust in accounting for variability that may arise due to tissue quality, handling and storage, cell growth conditions, or any mitochondrial proliferation that may be present in tissues from patients with mitochondrial disease. Considerations for adaption of these techniques to other cells, tissues, and organisms are presented, as well as comparisons to alternate methods for analysis of respiratory chain function. In this context, a quantitative immunofluorescence protocol is also provided that is suitable for measurement of the amount of multiple respiratory chain complexes in small diagnostic tissue samples. The analysis and interpretation of OXPHOS enzyme activities are then placed in the context of mitochondrial disease tissue pathology and diagnosis.
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Affiliation(s)
- Ann E Frazier
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David R Thorburn
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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39
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Rius R, Van Bergen NJ, Compton AG, Riley LG, Kava MP, Balasubramaniam S, Amor DJ, Fanjul-Fernandez M, Cowley MJ, Fahey MC, Koenig MK, Enns GM, Sadedin S, Wilson MJ, Tan TY, Thorburn DR, Christodoulou J. Clinical Spectrum and Functional Consequences Associated with Bi-Allelic Pathogenic PNPT1 Variants. J Clin Med 2019; 8:jcm8112020. [PMID: 31752325 PMCID: PMC6912252 DOI: 10.3390/jcm8112020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 02/01/2023] Open
Abstract
PNPT1 (PNPase—polynucleotide phosphorylase) is involved in multiple RNA processing functions in the mitochondria. Bi-allelic pathogenic PNPT1 variants cause heterogeneous clinical phenotypes affecting multiple organs without any established genotype–phenotype correlations. Defects in PNPase can cause variable combined respiratory chain complex defects. Recently, it has been suggested that PNPase can lead to activation of an innate immune response. To better understand the clinical and molecular spectrum of patients with bi-allelic PNPT1 variants, we captured detailed clinical and molecular phenotypes of all 17 patients reported in the literature, plus seven new patients, including a 78-year-old male with the longest reported survival. A functional follow-up of genomic sequencing by cDNA studies confirmed a splicing defect in a novel, apparently synonymous, variant. Patient fibroblasts showed an accumulation of mitochondrial unprocessed PNPT1 transcripts, while blood showed an increased interferon response. Our findings suggest that functional analyses of the RNA processing function of PNPase are more sensitive than testing downstream defects in oxidative phosphorylation (OXPHPOS) enzyme activities. This research extends our knowledge of the clinical and functional consequences of bi-allelic pathogenic PNPT1 variants that may guide management and further efforts into understanding the pathophysiological mechanisms for therapeutic development.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Nicole J. Van Bergen
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Lisa G. Riley
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Shanti Balasubramaniam
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
- Genetic Metabolic Disorders Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia
| | - David J. Amor
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Miriam Fanjul-Fernandez
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - Michael C. Fahey
- Department of Paediatrics, Monash University, Melbourne, VIC 3168, Australia
| | - Mary K. Koenig
- The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Gregory M. Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA 94305, USA
| | - Simon Sadedin
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Meredith J. Wilson
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Tiong Y. Tan
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +613-9936-6353
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Kang Y, Anderson AJ, Jackson TD, Palmer CS, De Souza DP, Fujihara KM, Stait T, Frazier AE, Clemons NJ, Tull D, Thorburn DR, McConville MJ, Ryan MT, Stroud DA, Stojanovski D. Function of hTim8a in complex IV assembly in neuronal cells provides insight into pathomechanism underlying Mohr-Tranebjærg syndrome. eLife 2019; 8:48828. [PMID: 31682224 PMCID: PMC6861005 DOI: 10.7554/elife.48828] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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] [Received: 05/28/2019] [Accepted: 11/04/2019] [Indexed: 12/13/2022] Open
Abstract
Human Tim8a and Tim8b are members of an intermembrane space chaperone network, known as the small TIM family. Mutations in TIMM8A cause a neurodegenerative disease, Mohr-Tranebjærg syndrome (MTS), which is characterised by sensorineural hearing loss, dystonia and blindness. Nothing is known about the function of hTim8a in neuronal cells or how mutation of this protein leads to a neurodegenerative disease. We show that hTim8a is required for the assembly of Complex IV in neurons, which is mediated through a transient interaction with Complex IV assembly factors, in particular the copper chaperone COX17. Complex IV assembly defects resulting from loss of hTim8a leads to oxidative stress and changes to key apoptotic regulators, including cytochrome c, which primes cells for death. Alleviation of oxidative stress with Vitamin E treatment rescues cells from apoptotic vulnerability. We hypothesise that enhanced sensitivity of neuronal cells to apoptosis is the underlying mechanism of MTS.
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Affiliation(s)
- Yilin Kang
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Thomas Daniel Jackson
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Catherine S Palmer
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - David P De Souza
- Metabolomics Australia, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Kenji M Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Tegan Stait
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Deidreia Tull
- Metabolomics Australia, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetic Services, Royal Children's Hospital, Melbourne, Australia
| | - Malcolm J McConville
- Metabolomics Australia, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
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41
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Van Bergen NJ, Guo Y, Rankin J, Paczia N, Becker-Kettern J, Kremer LS, Pyle A, Conrotte JF, Ellaway C, Procopis P, Prelog K, Homfray T, Baptista J, Baple E, Wakeling M, Massey S, Kay DP, Shukla A, Girisha KM, Lewis LES, Santra S, Power R, Daubeney P, Montoya J, Ruiz-Pesini E, Kovacs-Nagy R, Pritsch M, Ahting U, Thorburn DR, Prokisch H, Taylor RW, Christodoulou J, Linster CL, Ellard S, Hakonarson H. NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses. Brain 2019; 142:50-58. [PMID: 30576410 DOI: 10.1093/brain/awy310] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Physical stress, including high temperatures, may damage the central metabolic nicotinamide nucleotide cofactors [NAD(P)H], generating toxic derivatives [NAD(P)HX]. The highly conserved enzyme NAD(P)HX dehydratase (NAXD) is essential for intracellular repair of NAD(P)HX. Here we present a series of infants and children who suffered episodes of febrile illness-induced neurodegeneration or cardiac failure and early death. Whole-exome or whole-genome sequencing identified recessive NAXD variants in each case. Variants were predicted to be potentially deleterious through in silico analysis. Reverse-transcription PCR confirmed altered splicing in one case. Subject fibroblasts showed highly elevated concentrations of the damaged cofactors S-NADHX, R-NADHX and cyclic NADHX. NADHX accumulation was abrogated by lentiviral transduction of subject cells with wild-type NAXD. Subject fibroblasts and muscle biopsies showed impaired mitochondrial function, higher sensitivity to metabolic stress in media containing galactose and azide, but not glucose, and decreased mitochondrial reactive oxygen species production. Recombinant NAXD protein harbouring two missense variants leading to the amino acid changes p.(Gly63Ser) and p.(Arg608Cys) were thermolabile and showed a decrease in Vmax and increase in KM for the ATP-dependent NADHX dehydratase activity. This is the first study to identify pathogenic variants in NAXD and to link deficient NADHX repair with mitochondrial dysfunction. The results show that NAXD deficiency can be classified as a metabolite repair disorder in which accumulation of damaged metabolites likely triggers devastating effects in tissues such as the brain and the heart, eventually leading to early childhood death.
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Affiliation(s)
- Nicole J Van Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Julia Rankin
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Julia Becker-Kettern
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laura S Kremer
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carolyn Ellaway
- Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Genetic Medicine, University of Sydney, Sydney, Australia.,Neurology Department, Children's Hospital at Westmead, Sydney, Australia
| | - Peter Procopis
- Neurology Department, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Australia
| | - Kristina Prelog
- Medical Imaging Department, Children's Hospital at Westmead, Sydney, Australia
| | - Tessa Homfray
- Royal Brompton and St George's University Hospital, London, UK
| | - Júlia Baptista
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Emma Baple
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | | | - Sean Massey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia
| | - Daniel P Kay
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E S Lewis
- Department of Paediatrics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | | | | | - Piers Daubeney
- Royal Brompton Hospital, London, UK.,National Heart and Lung Institute, Imperial College, London, UK
| | - Julio Montoya
- Departamento de Bioquimica y Biologia Molecular y Celular- CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IISAragon), Universidad Zaragoza, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquimica y Biologia Molecular y Celular- CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IISAragon), Universidad Zaragoza, Zaragoza, Spain
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Martin Pritsch
- Department of Pediatric Neurology, DRK-Childrens-Hospital, Siegen, Germany
| | - Uwe Ahting
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Genetic Medicine, University of Sydney, Sydney, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Sian Ellard
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA USA
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Akesson LS, Eggers S, Love CJ, Chong B, Krzesinski EI, Brown NJ, Tan TY, Richmond CM, Thorburn DR, Christodoulou J, Hunter MF, Lunke S, Stark Z. Early diagnosis of Pearson syndrome in neonatal intensive care following rapid mitochondrial genome sequencing in tandem with exome sequencing. Eur J Hum Genet 2019; 27:1821-1826. [PMID: 31358953 DOI: 10.1038/s41431-019-0477-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 06/23/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023] Open
Abstract
Rapid genomic testing is a valuable new diagnostic tool for acutely unwell infants, however exome sequencing does not deliver clinical-grade mitochondrial genome sequencing and may fail to diagnose mitochondrial disorders caused by mitochondrial DNA (mtDNA) variants. Rapid mitochondrial genome sequencing and analysis are not routinely available in rapid genomic diagnosis programmes. We present two critically ill neonates with transfusion-dependent anaemia and persistent lactic acidosis who underwent rapid mitochondrial genome sequencing in tandem with exome sequencing as part of an exome sequencing-based rapid genomic diagnosis programme. No diagnostic variants were identified on examination of the nuclear exome data for either infant. Mitochondrial genome sequencing identified a large mtDNA deletion in both infants, diagnosing Pearson syndrome within 74 and 55 h, respectively. Early diagnosis in the third week of life allowed the avoidance of a range of other investigations and appropriate treatment planning. Rapid mitochondrial genome analysis provides additional diagnostic and clinical utility and should be considered as an adjunct to exome sequencing in rapid genomic diagnosis programmes.
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Affiliation(s)
- Lauren S Akesson
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Monash Genetics, Monash Medical Centre, Melbourne, VIC, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Clare J Love
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Emma I Krzesinski
- Monash Genetics, Monash Medical Centre, Melbourne, VIC, Australia.,Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Christopher M Richmond
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Medical Centre, Melbourne, VIC, Australia.,Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia. .,Australian Genomics Health Alliance, Melbourne, VIC, Australia.
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Frazier AE, Holt IJ, Spinazzola A, Thorburn DR. Reply: Genotype-phenotype correlation in ATAD3A deletions: not just of scientific relevance. Brain 2019; 140:e67. [PMID: 29053800 DOI: 10.1093/brain/awx240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Ian J Holt
- Biodonostia Health Research Institute, 20014 San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Antonella Spinazzola
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
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Lake NJ, Formosa LE, Stroud DA, Ryan MT, Calvo SE, Mootha VK, Morar B, Procopis PG, Christodoulou J, Compton AG, Thorburn DR. A patient with homozygous nonsense variants in two Leigh syndrome disease genes: Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant. Hum Mutat 2019; 40:893-898. [PMID: 30981218 DOI: 10.1002/humu.23753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 07/02/2018] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 01/04/2023]
Abstract
Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.
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Affiliation(s)
- Nicole J Lake
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Sarah E Calvo
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vamsi K Mootha
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bharti Morar
- Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, Western Australia, Australia.,Mitochondrial Medicine and Biology, Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Peter G Procopis
- Department of Neurology, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Alison G Compton
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Mitochondrial Laboratory, Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
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45
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Parikh S, Karaa A, Goldstein A, Bertini ES, Chinnery PF, Christodoulou J, Cohen BH, Davis RL, Falk MJ, Fratter C, Horvath R, Koenig MK, Mancuso M, McCormack S, McCormick EM, McFarland R, Nesbitt V, Schiff M, Steele H, Stockler S, Sue C, Tarnopolsky M, Thorburn DR, Vockley J, Rahman S. Diagnosis of 'possible' mitochondrial disease: an existential crisis. J Med Genet 2019; 56:123-130. [PMID: 30683676 DOI: 10.1136/jmedgenet-2018-105800] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 10/12/2018] [Revised: 12/11/2018] [Accepted: 12/23/2018] [Indexed: 02/02/2023]
Abstract
Primary genetic mitochondrial diseases are often difficult to diagnose, and the term 'possible' mitochondrial disease is used frequently by clinicians when such a diagnosis is suspected. There are now many known phenocopies of mitochondrial disease. Advances in genomic testing have shown that some patients with a clinical phenotype and biochemical abnormalities suggesting mitochondrial disease may have other genetic disorders. In instances when a genetic diagnosis cannot be confirmed, a diagnosis of 'possible' mitochondrial disease may result in harm to patients and their families, creating anxiety, delaying appropriate diagnosis and leading to inappropriate management or care. A categorisation of 'diagnosis uncertain', together with a specific description of the metabolic or genetic abnormalities identified, is preferred when a mitochondrial disease cannot be genetically confirmed.
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Affiliation(s)
- Sumit Parikh
- Mitochondrial Medicine Center, Neurologic Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Amel Karaa
- Genetics Unit, Mitochondrial Disease Program, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Amy Goldstein
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Enrico Silvio Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - John Christodoulou
- Neurodevelopmental Genomics Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
| | - Bruce H Cohen
- Department of Pediatrics and Rebecca D. Considine Research Institute, Akron Children's Hospital, Akron, Ohio, USA.,Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Ryan L Davis
- Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia.,Department of Neurogenetics, Koling Institute, University of Sydney and Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carl Fratter
- NHS Specialized Services for Rare Mitochondrial Disorders of Adults and Children UK, Oxford, UK.,Oxford Medical Genetics Laboratories, Oxford University, Oxford, UK
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mary Kay Koenig
- Department of Pediatrics, Mitochondrial Center, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Michaelangelo Mancuso
- Department of Experimental and Clinical Medicine, Neurological Institute, University of Pisa, Pisa, Italy
| | - Shana McCormack
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Robert McFarland
- Institute of Neurosciences, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
| | - Victoria Nesbitt
- Institute of Neurosciences, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Oxford University Hospitals, Oxford, UK
| | - Manuel Schiff
- Reference Center for Inborn Errors of Metabolism, Robert-Debré University Hospital, APHP, UMR1141, PROTECT, INSERM, Université Paris-Diderot, Paris, France
| | - Hannah Steele
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Department of Neurology, Sunderland Royal Hospital, Sunderland, UK
| | - Silvia Stockler
- Department of Pediatrics, Division of Biochemical Diseases, University of British Columbia, Vancouver, Canada
| | - Carolyn Sue
- Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia.,Department of Neurogenetics, Koling Institute, University of Sydney and Royal North Shore Hospital, Sydney, New South Wales, Australia.,Department of Neurology, Royal North Shore Hospital, Sydney, NewSouth Wales, Australia
| | - Mark Tarnopolsky
- Department of Pediatrics, Neuromuscular and Neurometabolic Clinic, McMaster University, Hamilton, Ontario, Canada
| | - David R Thorburn
- Royal Children's Hospital, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine; Center for Rare Disease Therapy, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK.,Metabolic Unit, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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46
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Hayhurst H, de Coo IFM, Piekutowska-Abramczuk D, Alston CL, Sharma S, Thompson K, Rius R, He L, Hopton S, Ploski R, Ciara E, Lake NJ, Compton AG, Delatycki MB, Verrips A, Bonnen PE, Jones SA, Morris AA, Shakespeare D, Christodoulou J, Wesol-Kucharska D, Rokicki D, Smeets HJM, Pronicka E, Thorburn DR, Gorman GS, McFarland R, Taylor RW, Ng YS. Leigh syndrome caused by mutations in MTFMT is associated with a better prognosis. Ann Clin Transl Neurol 2019; 6:515-524. [PMID: 30911575 PMCID: PMC6414492 DOI: 10.1002/acn3.725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022] Open
Abstract
Objectives Mitochondrial methionyl‐tRNA formyltransferase (MTFMT) is required for the initiation of translation and elongation of mitochondrial protein synthesis. Pathogenic variants in MTFMT have been associated with Leigh syndrome (LS) and mitochondrial multiple respiratory chain deficiencies. We sought to elucidate the spectrum of clinical, neuroradiological and molecular genetic findings of patients with bi‐allelic pathogenic variants in MTFMT. Methods Retrospective cohort study combining new cases and previously published cases. Results Thirty‐eight patients with pathogenic variants in MTFMT were identified, including eight new cases. The median age of presentation was 14 months (range: birth to 17 years, interquartile range [IQR] 4.5 years), with developmental delay and motor symptoms being the most frequent initial manifestation. Twenty‐nine percent of the patients survived into adulthood. MRI headings in MTFMT pathogenic variants included symmetrical basal ganglia changes (62%), periventricular and subcortical white matter abnormalities (55%), and brainstem lesions (48%). Isolated complex I and combined respiratory chain deficiencies were identified in 31% and 59% of the cases, respectively. Reduction of the mitochondrial complex I and complex IV subunits was identified in the fibroblasts (13/13). Sixteen pathogenic variants were identified, of which c.626C>T was the most common. Seventy‐four percent of the patients were alive at their last clinical review (median 6.8 years, range: 14 months to 31 years, IQR 14.5 years). Interpretation Patients that harbour pathogenic variants in MTFMT have a milder clinical phenotype and disease progression compared to LS caused by other nuclear defects. Fibroblasts may preclude the need for muscle biopsy, to prove causality of any novel variant.
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Affiliation(s)
- Hannah Hayhurst
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Irenaeus F M de Coo
- Department of Neurology Erasmus Medical Centre Rotterdam Netherlands.,Department of Paediatrics, Nutrition and Metabolic Diseases The Children's Memorial Health Institute Warsaw Poland
| | | | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Sunil Sharma
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Rocio Rius
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Langping He
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Rafal Ploski
- Department of Medical Genetics The Children's Memorial Health Institute Warsaw 04-730 Poland
| | - Elzbieta Ciara
- Department of Medical Genetics The Children's Memorial Health Institute Warsaw 04-730 Poland
| | - Nicole J Lake
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Alison G Compton
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Aad Verrips
- Department of Neurology Canisius Wilhelmina Hospital Nijmegen The Netherlands
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Simon A Jones
- Manchester Centre for Genomic Medicine Manchester University NHS Foundation Trust Manchester Academic Health Sciences Centre Manchester UK
| | - Andrew A Morris
- Manchester Centre for Genomic Medicine Manchester University NHS Foundation Trust Manchester Academic Health Sciences Centre Manchester UK
| | - David Shakespeare
- Neuro-Rehabilitation Unit Royal Preston Hospital Preston United Kingdom
| | - John Christodoulou
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Dorota Wesol-Kucharska
- Department of Clinical Genomics Research Schools GROW and MHeNS Maastricht University Maastricht The Netherlands
| | - Dariusz Rokicki
- Department of Clinical Genomics Research Schools GROW and MHeNS Maastricht University Maastricht The Netherlands
| | - Hubert J M Smeets
- Department of Paediatrics, Nutrition and Metabolic Diseases The Children's Memorial Health Institute Warsaw Poland
| | - Ewa Pronicka
- Department of Medical Genetics The Children's Memorial Health Institute Warsaw 04-730 Poland.,Neuro-Rehabilitation Unit Royal Preston Hospital Preston United Kingdom
| | - David R Thorburn
- Victorian Clinical Genetics Service and Murdoch Children's Research Institute Parkville Victoria 3052 Australia.,Department of Paediatrics University of Melbourne Melbourne Victoria 3052 Australia
| | - Grainne S Gorman
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research Institute of Neuroscience Newcastle University Newcastle upon Tyne United Kingdom
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47
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Akesson LS, Eggers S, Chong B, Hunter MF, Krzesinski E, Brown NJ, Tan TY, Richmond C, Thorburn DR, Christodoulou J, Stark Z, Lunke S. Rapid mitochondrial genome (MTDNA) sequencing: facilitating rapid diagnosis of mitochondrial diseases in paediatric acute care. Pathology 2019. [DOI: 10.1016/j.pathol.2018.12.339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Rius R, Riley LG, Guo Y, Menezes M, Compton AG, Van Bergen NJ, Gayevskiy V, Cowley MJ, Cummings BB, Adams L, Ellaway C, Thorburn DR, Hakonarson H, Christodoulou J. Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child. Mol Genet Metab 2019; 126:77-82. [PMID: 30558828 DOI: 10.1016/j.ymgme.2018.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND In almost half of patients with acute liver failure the cause is unknown, making targeted treatment and decisions about liver transplantation a challenge. Monogenic disorders may contribute to a significant proportion of these undiagnosed patients, and so the incorporation of technologies such as next generation sequencing (NGS) in the clinic could aid in providing a definitive diagnosis. However, this technology may present a major challenge in interpretation of sequence variants, particularly those in non-coding regions. RESULTS In this report we describe a case of Infantile liver failure syndrome 2 (ILFS2; MIM 616483) due to novel bi-allelic variants in the NBAS gene. A missense variant NM_015909.3(NBAS):c.2617C > T, NP_056993.2(NBAS):p.(Arg873Trp) was identified by whole genome sequencing (WGS). By combining WGS and reverse transcription-polymerase chain reaction (RT-PCR) we were able to identify a novel deep intronic variant, NM_015909.3(NBAS):c.2423 + 404G > C, leading to the inclusion of a pseudo-exon. This mechanism has not been described previously in this syndrome. CONCLUSIONS This study highlights the utility of analyzing NGS data in conjunction with investigating complementary DNA (cDNA) using techniques such as RT-PCR for detection of variants that otherwise would be likely to be missed in common NGS bioinformatic analysis pipelines. Combining these approaches, particularly when the phenotype match is strong, could lead to an increase in the diagnostic yield in acute liver failure and thus aid in targeted treatment, accurate genetic counseling and restoration of reproductive confidence.
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Affiliation(s)
- Rocio Rius
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lisa G Riley
- Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Minal Menezes
- Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Alison G Compton
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Nicole J Van Bergen
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, Australia; Children's Cancer Institute, Kensington, Australia
| | - Beryl B Cummings
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, USA
| | - Louisa Adams
- Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Carolyn Ellaway
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, Australia; Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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49
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Loetsch C, Warren J, Laskowski A, Vazquez-Lombardi R, Jandl C, Langley DB, Christ D, Thorburn DR, Ryugo DK, Sprent J, Batten M, King C. Cytosolic Recognition of RNA Drives the Immune Response to Heterologous Erythrocytes. Cell Rep 2018; 21:1624-1638. [PMID: 29117566 DOI: 10.1016/j.celrep.2017.10.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/07/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
The archetypal T cell-dependent antigen is sheep red blood cells (SRBCs), which have defined much of what we know about humoral immunity. Early studies using solubilized or sonicated SRBCs argued that the intact structure of SRBCs was important for optimal antibody responses. However, the reason for the requirement of intact SRBCs for the response to polyvalent protein antigen remained unknown. Here, we report that the immune response to SRBCs is driven by cytosolic recognition of SRBC RNA through the RIG-I-like receptor (RLR)-mitochondrial anti-viral signaling adaptor (MAVS) pathway. Following the uptake of SRBCs by antigen-presenting cells, the MAVS signaling complex governs the differentiation of both T follicular cells and antibody-producing B cells. Importantly, the involvement of the RLR-MAVS pathway precedes that of endosomal Toll-like receptor pathways, yet both are required for optimal effect.
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Affiliation(s)
- Claudia Loetsch
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Warren
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia
| | - Adrienne Laskowski
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia
| | - Rodrigo Vazquez-Lombardi
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Christoph Jandl
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - David B Langley
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Daniel Christ
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville VIC 3010, Australia
| | - David K Ryugo
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Jonathan Sprent
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcel Batten
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Cecile King
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia.
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50
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Stutterd CA, Lake NJ, Peters H, Lockhart PJ, Taft RJ, van der Knaap MS, Vanderver A, Thorburn DR, Simons C, Leventer RJ. Severe Leukoencephalopathy with Clinical Recovery Caused by Recessive BOLA3 Mutations. JIMD Rep 2018; 43:63-70. [PMID: 29654549 DOI: 10.1007/8904_2018_100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 03/10/2023] Open
Abstract
AIM To identify the genetic aetiology of a distinct leukoencephalopathy causing acute neurological regression in infancy with apparently complete clinical recovery. METHODS We performed trio whole genome sequencing (WGS) to determine the genetic basis of the disorder. Mitochondrial function analysis in cultured patient fibroblasts was undertaken to confirm the pathogenicity of candidate variants. RESULTS The patient presented at 18 months with acute hemiplegia and cognitive regression without obvious trigger. This was followed by clinical recovery over 4 years. MRI at disease onset revealed bilateral T2 hyperintensity involving the periventricular and deep white matter and MR spectroscopy of frontal white matter demonstrated a lactate doublet. Lactate levels and mitochondrial respiratory chain enzyme activity in muscle, liver and fibroblasts were normal. Plasma glycine was elevated. The MRI abnormalities improved. WGS identified compound heterozygous variants in BOLA3: one previously reported (c.136C>T, p.Arg46*) and one novel variant (c.176G>A, p.Cys59Tyr). Analysis of cultured patient fibroblasts demonstrated deficient pyruvate dehydrogenase (PDH) activity and reduced quantity of protein subunits of mitochondrial complexes I and II, consistent with BOLA3 dysfunction. Previously reported cases of multiple mitochondrial dysfunctions syndrome 2 (MMDS2) with hyperglycinaemia caused by BOLA3 mutations have leukodystrophy with severe, progressive neurological and multisystem disease. CONCLUSIONS We report a novel phenotype for MMDS2 associated with apparently complete clinical recovery and partial resolution of MRI abnormalities. We have identified a novel disease-causing variant in BOLA3 validated by functional cellular studies. Our patient's clinical course broadens the phenotypic spectrum of MMDS2 and highlights the potential for some genetic leukoencephalopathies to spontaneously improve.
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Affiliation(s)
- C A Stutterd
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Department of Neurology, Royal Children's Hospital, Parkville, VIC, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
| | - N J Lake
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Mitochondrial Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - H Peters
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Metabolic Medicine, Royal Children's Hospital, Parkville, VIC, Australia
- Metabolic Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - P J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - R J Taft
- Illumina Inc, San Diego, CA, USA
| | - M S van der Knaap
- Department of Child Neurology, VU University Medical Center, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
| | - A Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Mitochondrial Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - C Simons
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
- Translational Bioinformatics Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - R J Leventer
- Department of Neurology, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Neuroscience Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
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