title: Whole-exome sequencing identifies novel variants in PNPT1 causing oxidative phosphorylation defects and severe multisystem disease.
abstract: Recent advances in next-generation sequencing strategies have led to the discovery of many novel disease genes. We describe here a non-consanguineous family with two affected boys presenting with early onset of severe axonal neuropathy, optic atrophy, intellectual disability, auditory neuropathy and chronic respiratory and gut disturbances. Whole-exome sequencing (WES) was performed on all family members and we identified compound heterozygous variants (c.[760C>A];[1528G>C];p.[(Gln254Lys);(Ala510Pro)] in the polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene in both affected individuals. PNPT1 encodes the polynucleotide phosphorylase (PNPase) protein, which is involved in the transport of small RNAs into the mitochondria. These RNAs are involved in the mitochondrial translation machinery, responsible for the synthesis of mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) complexes. Both PNPT1 variants are within highly conserved regions and predicted to be damaging. These variants resulted in quaternary defects in the PNPase protein and a clear reduction in protein and mRNA expression of PNPT1 in patient fibroblasts compared with control cells. Protein analysis of the OXPHOS complexes showed a significant reduction in complex I (CI), complex III (CIII) and complex IV (CIV). Enzyme activity of CI and CIV was clearly reduced in patient fibroblasts compared with controls along with a 33% reduction in total mitochondrial protein synthesis. In vitro rescue experiments, using exogenous expression of wild-type PNPT1 in patient fibroblasts, ameliorated the deficiencies in the OXPHOS complex protein expression, supporting the likely pathogenicity of these variants and the importance of WES in efficiently identifying rare genetic disease genes.
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.|Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.|Genetic Metabolic Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Alodaib
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Nara
authors.initials: N
authors.lastname: Sobreira
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.|Genetic Metabolic Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Gold
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.|Genetic Metabolic Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
authors.forename: Lisa G
authors.initials: LG
authors.lastname: Riley
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia.
authors.forename: Nicole J
authors.initials: NJ
authors.lastname: Van Bergen
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.|Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.|Clinical Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
authors.forename: Meredith J
authors.initials: MJ
authors.lastname: Wilson
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.|Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.|Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
authors.forename: Bruce
authors.initials: B
authors.lastname: Bennetts
authors.affiliation: Murdoch Childrens 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.
authors.forename: David R
authors.initials: DR
authors.lastname: Thorburn
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Corinne
authors.initials: C
authors.lastname: Boehm
authors.affiliation: Disciplines of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia. john.christodoulou@mcri.edu.au.|Genetic Metabolic Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia. john.christodoulou@mcri.edu.au.|Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia. john.christodoulou@mcri.edu.au.|Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia. john.christodoulou@mcri.edu.au.|Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, Australia. john.christodoulou@mcri.edu.au.|Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia. john.christodoulou@mcri.edu.au.
authors.forename: John
authors.initials: J
authors.lastname: Christodoulou
mesh_terms: D001369:Axons / Q000473:pathology; D059472:Exome / Q000235:genetics; D005095:Exoribonucleases / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics* / Q000503:physiopathology; D008297:Male; D008928:Mitochondria / Q000235:genetics / Q000473:pathology; D009154:Mutation; D009896:Optic Atrophy / Q000235:genetics* / Q000503:physiopathology; D010085:Oxidative Phosphorylation; D010375:Pedigree; D020836:Protein Structure, Quaternary; D024101:Mitochondrial Proteins
chemical_list: D005095:Exoribonucleases; C476417:PNPT1 protein, human; D024101:Mitochondrial Proteins