Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient

David K Miller; Minal J Menezes; Cas Simons; Lisa G Riley; Sandra T Cooper; Sean M Grimmond; David R Thorburn; John Christodoulou; Ryan J Taft

doi:10.1371/journal.pone.0104879

Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient

PLoS One. 2014 Aug 12;9(8):e104879. doi: 10.1371/journal.pone.0104879. eCollection 2014.

Authors

David K Miller¹, Minal J Menezes², Cas Simons³, Lisa G Riley⁴, Sandra T Cooper⁵, Sean M Grimmond¹, David R Thorburn⁶, John Christodoulou⁷, Ryan J Taft⁸

Affiliations

¹ Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
² Genetic Metabolic Disorders Research Unit, Kids Research Institute, Children's Hospital at Westmead, Sydney, Westmead New South Wales, Australia; Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Camperdown New South Wales, Australia.
³ Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
⁴ Genetic Metabolic Disorders Research Unit, Kids Research Institute, Children's Hospital at Westmead, Sydney, Westmead New South Wales, Australia.
⁵ Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Camperdown New South Wales, Australia; Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia.
⁶ Murdoch Childrens Research Institute and Victorian Clinical Genetics Services, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
⁷ Genetic Metabolic Disorders Research Unit, Kids Research Institute, Children's Hospital at Westmead, Sydney, Westmead New South Wales, Australia; Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Camperdown New South Wales, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia.
⁸ Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia; Departments of Integrative Systems Biology and Pediatrics, George Washington University School of Medicine, Washington, D.C., United States of America.

Abstract

Leigh syndrome (LS) is a rare progressive multi-system neurodegenerative disorder, the genetics of which is frequently difficult to resolve. Rapid determination of the genetic etiology of LS in a 5-year-old girl facilitated inclusion in Edison Pharmaceutical's phase 2B clinical trial of EPI-743. SNP-arrays and high-coverage whole exome sequencing were performed on the proband, both parents and three unaffected siblings. Subsequent multi-tissue targeted high-depth mitochondrial sequencing was performed using custom long-range PCR amplicons. Tissue-specific mutant load was also assessed by qPCR. Complex I was interrogated by spectrophotometric enzyme assays and Western Blot. No putatively causal mutations were identified in nuclear-encoded genes. Analysis of low-coverage off-target mitochondrial reads revealed a previously unreported mitochondrial mutation in the proband in MT-ND3 (m.10134C>A, p.Q26K), a Complex I mitochondrial gene previously associated with LS. Targeted investigations demonstrated that this mutation was 1% heteroplasmic in the mother's blood and homoplasmic in the proband's blood, fibroblasts, liver and muscle. Enzyme assays revealed decreased Complex I activity. The identification of this novel LS MT-ND3 variant, the genomics of which was accomplished in less than 3.5 weeks, indicates that rapid genomic approaches may prove useful in time-sensitive cases with an unresolved genetic diagnosis.

Publication types

Case Reports
Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Substitution
Brain / pathology
Child, Preschool
DNA Mutational Analysis
DNA, Mitochondrial / genetics*
Electron Transport Complex I / genetics*
Electron Transport Complex I / metabolism
Exome / genetics
Female
Genes, Mitochondrial
High-Throughput Nucleotide Sequencing
Humans
Leigh Disease / diagnosis
Leigh Disease / genetics*
Leigh Disease / metabolism
Magnetic Resonance Imaging
Male
Mutant Proteins / genetics
Mutant Proteins / metabolism
Mutation, Missense*
Pedigree
Polymorphism, Single Nucleotide

Substances

DNA, Mitochondrial
Mutant Proteins
Electron Transport Complex I
MT-ND3 protein, human

Grants and funding

The authors thank Illumina Inc. for their support of this project, and the Queensland Center for Medical Genomics and the IMB Sequencing Core for their assistance. This research was supported by National Health and Medical Research Council of Australia (NHMRC) Project Grant 1026891, and a University of Queensland Foundation Research Excellence Award to RJT. MM is an Australian Mitochondrial Diseases Foundation (AMDF) Postgraduate Research Scholar. DRT is an NHMRC Principal Research Fellow. The authors thank Wendy Fagan for assistance with enzyme assays and are grateful to the Crane and Perkins families for their generous financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.