Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype

Thomas B Smith; Robert Kopajtich; Leigh A M Demain; Alessandro Rea; Huw B Thomas; Manuel Schiff; Christian Beetz; Shelagh Joss; Gerard S Conway; Anju Shukla; Mayuri Yeole; Periyasamy Radhakrishnan; Hatem Azzouz; Amel Ben Chehida; Monique Elmaleh-Bergès; Ruth I C Glasgow; Kyle Thompson; Monika Oláhová; Langping He; Emma M Jenkinson; Amir Jahic; Inna A Belyantseva; Melanie Barzik; Jill E Urquhart; James O'Sullivan; Simon G Williams; Sanjeev S Bhaskar; Samantha Carrera; Alexander J M Blakes; Siddharth Banka; Wyatt W Yue; Jamie M Ellingford; Henry Houlden; DDD Study; Kevin J Munro; Thomas B Friedman; Robert W Taylor; Holger Prokisch; Raymond T O'Keefe; William G Newman

doi:10.1016/j.ajhg.2024.11.007

Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype

Am J Hum Genet. 2024 Dec 14:S0002-9297(24)00416-6. doi: 10.1016/j.ajhg.2024.11.007. Online ahead of print.

Authors

Thomas B Smith¹, Robert Kopajtich², Leigh A M Demain¹, Alessandro Rea¹, Huw B Thomas¹, Manuel Schiff³, Christian Beetz⁴, Shelagh Joss⁵, Gerard S Conway⁶, Anju Shukla⁷, Mayuri Yeole⁷, Periyasamy Radhakrishnan⁷, Hatem Azzouz⁸, Amel Ben Chehida⁹, Monique Elmaleh-Bergès¹⁰, Ruth I C Glasgow¹¹, Kyle Thompson¹², Monika Oláhová¹³, Langping He¹⁴, Emma M Jenkinson¹, Amir Jahic¹⁵, Inna A Belyantseva¹⁶, Melanie Barzik¹⁶, Jill E Urquhart¹, James O'Sullivan¹, Simon G Williams¹, Sanjeev S Bhaskar¹, Samantha Carrera¹⁷, Alexander J M Blakes¹, Siddharth Banka¹, Wyatt W Yue¹⁸, Jamie M Ellingford¹⁹, Henry Houlden²⁰; DDD Study²¹; Kevin J Munro²², Thomas B Friedman¹⁶, Robert W Taylor²³, Holger Prokisch², Raymond T O'Keefe²⁴, William G Newman²⁵

Affiliations

¹ Division of Evolution, Infection and Genomics, School of Biological Sciences, the University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, the University of Manchester NHS Foundation Trust, Manchester M13 9WL, UK.
² Institute of Human Genetics, Computational Health Center, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany.
³ Université Paris Cité, Reference Center for Mitochondrial Disorders (CARAMMEL) and Reference Center Inborn Error of Metabolism, Department of Pediatrics, Necker-Enfants Malades Hospital, APHP, Filière G2M, Paris, France; INSERM UMR_S1163, Institut Imagine, Université Paris Cité, Paris, France.
⁴ Centogene GmbH, Rostock, Germany.
⁵ West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK.
⁶ Institute for Women's Health, University College London, London, UK.
⁷ Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
⁸ Service de Pédiatrie et des Maladies Métaboliques Héréditaires, Centre Hospitalier Universitaire la Rabta, Jabberi 1007, Tunis, Tunisia.
⁹ Laboratoire de Recherche LR12SP02, Maladies Métaboliques Héréditaires Investigations et Prise en Charge, Service de Pédiatrie et des Maladies Métaboliques Héréditaires, Centre Hospitalier Universitaire la Rabta, Jabberi 1007, Tunis, Tunisia.
¹⁰ Service de Radiologie Pédiatrique, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France.
¹¹ Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden.
¹² Mitochondrial Research Group, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
¹³ Mitochondrial Research Group, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
¹⁴ NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK.
¹⁵ Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
¹⁶ Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892-3729, USA.
¹⁷ Genome Editing Unit, University of Manchester, Manchester M13 9PT, UK.
¹⁸ Newcastle University Biosciences Institute, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
¹⁹ Division of Evolution, Infection and Genomics, School of Biological Sciences, the University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, the University of Manchester NHS Foundation Trust, Manchester M13 9WL, UK; Genomics England, London, UK.
²⁰ Department of Molecular Neuroscience, University College London Queen Square Institute of Neurology, London, UK.
²¹ Wellcome Trust Sanger Institute, Cambridge, UK.
²² Manchester Centre for Audiology and Deafness (ManCAD), School of Health Sciences, University of Manchester, Manchester, UK.
²³ Mitochondrial Research Group, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK.
²⁴ Division of Evolution, Infection and Genomics, School of Biological Sciences, the University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, the University of Manchester NHS Foundation Trust, Manchester M13 9WL, UK. Electronic address: [email protected].
²⁵ Division of Evolution, Infection and Genomics, School of Biological Sciences, the University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, the University of Manchester NHS Foundation Trust, Manchester M13 9WL, UK. Electronic address: [email protected].

PMID: 39701103
DOI: 10.1016/j.ajhg.2024.11.007

Abstract

The mitochondrial ribosome (mitoribosome) synthesizes 13 protein subunits of the oxidative phosphorylation system encoded by the mitochondrial genome. The mitoribosome is composed of 12S rRNA, 16S rRNA, and 82 mitoribosomal proteins encoded by nuclear genes. To date, variants in 12 genes encoding mitoribosomal proteins are associated with rare monogenic disorders and frequently show combined oxidative phosphorylation deficiency. Here, we describe five unrelated individuals with bi-allelic variants in death-associated protein 3 (DAP3), a nuclear gene encoding mitoribosomal small subunit 29 (MRPS29), with variable clinical presentations ranging from Perrault syndrome (sensorineural hearing loss and ovarian insufficiency) to an early childhood neurometabolic phenotype. Assessment of respiratory-chain function and proteomic profiling of fibroblasts from affected individuals demonstrated reduced MRPS29 protein amounts and, consequently, decreased levels of additional protein components of the mitoribosomal small subunit, as well as an associated combined deficiency of complexes I and IV. Lentiviral transduction of fibroblasts from affected individuals with wild-type DAP3 cDNA increased DAP3 mRNA expression and partially rescued protein levels of MRPS7, MRPS9, and complex I and IV subunits, demonstrating the pathogenicity of the DAP3 variants. Protein modeling suggested that DAP3 disease-associated missense variants can impact ADP binding, and in vitro assays demonstrated that DAP3 variants can consequently reduce both intrinsic and extrinsic apoptotic sensitivity, DAP3 thermal stability, and DAP3 GTPase activity. Our study presents genetic and functional evidence that bi-allelic variants in DAP3 result in a multisystem disorder of combined oxidative phosphorylation deficiency with pleiotropic presentations, consistent with mitochondrial dysfunction.

Keywords: DAP3; MRPS29; Perrault syndrome; leukodystrophy; mitochondria; mitoribosomal small subunit; mitoribosome; ovarian insufficiency; rare disease; sensorineural hearing loss.