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Nithianandam V, Sarkar S, Feany MB. Pathways controlling neurotoxicity and proteostasis in mitochondrial complex I deficiency. Hum Mol Genet 2024; 33:860-871. [PMID: 38324746 PMCID: PMC11070137 DOI: 10.1093/hmg/ddae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Neuromuscular disorders caused by dysfunction of the mitochondrial respiratory chain are common, severe and untreatable. We recovered a number of mitochondrial genes, including electron transport chain components, in a large forward genetic screen for mutations causing age-related neurodegeneration in the context of proteostasis dysfunction. We created a model of complex I deficiency in the Drosophila retina to probe the role of protein degradation abnormalities in mitochondrial encephalomyopathies. Using our genetic model, we found that complex I deficiency regulates both the ubiquitin/proteasome and autophagy/lysosome arms of the proteostasis machinery. We further performed an in vivo kinome screen to uncover new and potentially druggable mechanisms contributing to complex I related neurodegeneration and proteostasis failure. Reduction of RIOK kinases and the innate immune signaling kinase pelle prevented neurodegeneration in complex I deficiency animals. Genetically targeting oxidative stress, but not RIOK1 or pelle knockdown, normalized proteostasis markers. Our findings outline distinct pathways controlling neurodegeneration and protein degradation in complex I deficiency and introduce an experimentally facile model in which to study these debilitating and currently treatment-refractory disorders.
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Affiliation(s)
- Vanitha Nithianandam
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, 5425 Wisconsin Avenue, Chevy Chase, MD 20815, United States
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, 5425 Wisconsin Avenue, Chevy Chase, MD 20815, United States
| | - Mel B Feany
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, 5425 Wisconsin Avenue, Chevy Chase, MD 20815, United States
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Dasgupta S, Goodale B, Tanguay R. Single cell sequencing of zebrafish kidney marrows reveals AHR2-dependent endogenous regulation of hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590755. [PMID: 38712290 PMCID: PMC11071399 DOI: 10.1101/2024.04.23.590755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a wide range of biological and toxicological responses. While largely studied in ligand-activated toxicant responses, AHR also plays important roles in endogenous physiological processes. We leveraged single cell sequencing and an AHR2 knockout zebrafish line to investigate the role of AHR2 in regulating hematopoiesis (production and differentiation of red and white blood cells from hematopoietic stem cells). Our objectives were to determine if absence of AHR2- 1) alters proportions of immune cell populations and/or 2) impacts gene expression within individual immune cell types. We dissected kidney marrow (organ of hematopoiesis in zebrafish) from adult wildtype and AHR2 knockout zebrafish (N=3/genotype), isolated single cells and sequenced ~ 5000 cells/sample (10X Genomics). We identified 14 cell clusters representing the expected major blood (erythrocytes, thrombocytes), immune (B cells, macrophages, lymphoid cells, granulocytes, etc), progenitors and kidney cell populations. We focused our analyses only on the progenitor and mature immune cell types. While there were no genotype-specific differences in proportion of individual cell types, gene expression differences were observed within several cell types. For known genes, such as rrm2, changes were up to 2000-fold, signifying their importance in AHR2-hematopoesis interaction. Several of the known genes are also identified as markers of carcinoma cells for an array of cancer types. However, many of the dysregulated genes are poorly annotated, limiting our ability to examine biological processes and pathways dysregulated on AHR2 mutation. Nevertheless, our study indicates that AHR2 plays an important endogenous role in hematopoiesis. Future work will focus on better characterizing anatomy of dysregulated genes and their functions in hematopoiesis.
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Affiliation(s)
- Subham Dasgupta
- Department of Biological Sciences, Clemson University, Clemson, SC
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR
| | - Britton Goodale
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Robyn Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR
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Ou-Yang CH, Chen PS, Lin CH. Generation of a human induced pluripotent stem cell line NTUHi004-A from a patient with Leigh syndrome harboring a homozygous missense mutation c.836 T > G (p.Met279Arg) in NDUFAF5 gene. Stem Cell Res 2024; 76:103379. [PMID: 38458030 DOI: 10.1016/j.scr.2024.103379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
Leigh syndrome is a rare autosomal recessive disorder showcasing a diverse range of neurological symptoms. Classical Leigh syndrome is associated with mitochondrial complex I deficiency, primarily resulting from biallelic mutations in the NDUFAF5 gene, encoding the NADH:ubiquinone oxidoreductase complex assembly factor 5. Using the Sendai virus delivery system, we generated an induced pluripotent stem cell line from peripheral blood mononuclear cells of a 47-years-old female patient who carried a homozygous NDUFAF5 c.836 T > G (p.Met279Arg) mutation. This cellular model serves as a tool for investigating the underlying pathogenic mechanisms and for the development of potential treatments for Leigh syndrome.
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Affiliation(s)
- Chih-Hsin Ou-Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pin-Shiuan Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan; Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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Chen J, Wu Y, Yu S, Wan X, Gong Y, Sun X. Cognitive Impairment in Phenotypic Leber Hereditary Optic Neuropathy Caused by Mutation in Nuclear Gene NDUFAF5. J Neuroophthalmol 2024; 44:e20-e22. [PMID: 36580434 DOI: 10.1097/wno.0000000000001760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jieqiong Chen
- Department of Ophthalmology (JC, YW, SY, XW, YG, XS), Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center for Eye Diseases (JC, YW, SY, XW, YG, XS), Shanghai, China; Shanghai Key Laboratory of Fundus Diseases (XW, XS), Shanghai, China; and Shanghai Engineering Center for Visual Science and Photomedicine (XS), Shanghai, China
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Finsterer J. Before homozygous NDUFAF5 variants are held responsible for intrauterine death, their pathogenicity must be demonstrated. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:427-428. [PMID: 38340008 DOI: 10.1002/uog.27596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/11/2023] [Indexed: 02/12/2024]
Abstract
Linked article: This Correspondence comments on Brabbing‐Goldstein et al. Click here to view the article.
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Affiliation(s)
- J Finsterer
- Neurology & Neurophysiology Center, Vienna, Austria
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Brabbing-Goldstein D, Basel-Salmon L, Yaron Y. Reply. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:428-430. [PMID: 38426869 DOI: 10.1002/uog.27597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Affiliation(s)
- D Brabbing-Goldstein
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Ultrasound Unit, Helen Schneider Women's Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - L Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y Yaron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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Brabbing-Goldstein D, Kozlova D, Bazak L, Basel-Salmon L, Gilboa Y, Marciano-Levi I, Zahra J, Kanengisser-Pines B, Botvinik A, Kurolap A, Birnbaum R, Yaron Y. Unique prenatal manifestations of biallelic NDUFAF5 variants: expansion of phenotype. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:392-398. [PMID: 37718619 DOI: 10.1002/uog.27482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
OBJECTIVE Mitochondrial complex-I deficiency, nuclear type 16, is a rare autosomal recessive disorder caused by biallelic pathogenic variants in NDUFAF5 (C20orf7) (OMIM 618238). The aim of this study was to describe a severe early prenatal manifestation of this disorder, which was previously considered to occur only postnatally. METHODS This was a multicenter retrospective case series including five fetuses from three non-related families, which shared common sonographic abnormalities, including brain cysts, corpus callosal malformations, non-immune hydrops fetalis and growth restriction. Genetic evaluation included chromosomal microarray analysis and exome sequencing. Two fetuses from the same family were also available for pathology examination, including electron microscopy. RESULTS Chromosomal microarray analysis revealed no chromosomal abnormality in any of the tested cases. Trio exome sequencing demonstrated that three affected fetuses from three unrelated families were compound heterozygous or homozygous for likely pathogenic variants in NDUFAF5. No other causative variants were detected. The association between NDUFAF5 variants and fetal malformations was further confirmed by segregation analysis. Histological evaluation of fetal tissues and electron microscopy of the skeletal muscle, liver, proximal tubules and heart demonstrated changes that resembled postmortem findings in patients with mitochondrial depletion disorders as well as previously undescribed findings. CONCLUSIONS Mitochondrial complex-I deficiency and specifically biallelic mutations in NDUFAF5 have a role in abnormal fetal development, presenting with severe congenital malformations. Mitochondrial complex-I disorders should be considered in the differential diagnosis of corpus callosal malformations and brain cysts, especially when associated with extracranial abnormalities, such as fetal growth restriction and non-immune hydrops fetalis. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- D Brabbing-Goldstein
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Ultrasound Unit, Helen Schneider Women's Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - D Kozlova
- Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - L Bazak
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
| | - L Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y Gilboa
- Ultrasound Unit, Helen Schneider Women's Hospital, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - I Marciano-Levi
- Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - J Zahra
- Genetics Institute, Soroka Medical Center, Beer Sheva, Israel
| | | | - A Botvinik
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - A Kurolap
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - R Birnbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Ultrasound in Obstetrics and Gynecology, Lis Maternity and Hospital for Women's Health, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Y Yaron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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Granat L, Knorr DY, Ranson DC, Chakrabarty RP, Chandel NS, Bateman JM. A Drosophila model of mitochondrial disease phenotypic heterogeneity. Biol Open 2024; 13:bio060278. [PMID: 38304969 PMCID: PMC10924217 DOI: 10.1242/bio.060278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Mutations in genes that affect mitochondrial function cause primary mitochondrial diseases. Mitochondrial diseases are highly heterogeneous and even patients with the same mitochondrial disease can exhibit broad phenotypic heterogeneity, which is poorly understood. Mutations in subunits of mitochondrial respiratory complex I cause complex I deficiency, which can result in severe neurological symptoms and death in infancy. However, some complex I deficiency patients present with much milder symptoms. The most common nuclear gene mutated in complex I deficiency is the highly conserved core subunit NDUFS1. To model the phenotypic heterogeneity in complex I deficiency, we used RNAi lines targeting the Drosophila NDUFS1 homolog ND-75 with different efficiencies. Strong knockdown of ND-75 in Drosophila neurons resulted in severe behavioural phenotypes, reduced lifespan, altered mitochondrial morphology, reduced endoplasmic reticulum (ER)-mitochondria contacts and activation of the unfolded protein response (UPR). By contrast, weak ND-75 knockdown caused much milder behavioural phenotypes and changes in mitochondrial morphology. Moreover, weak ND-75 did not alter ER-mitochondria contacts or activate the UPR. Weak and strong ND-75 knockdown resulted in overlapping but distinct transcriptional responses in the brain, with weak knockdown specifically affecting proteosome activity and immune response genes. Metabolism was also differentially affected by weak and strong ND-75 knockdown including gamma-aminobutyric acid (GABA) levels, which may contribute to neuronal dysfunction in ND-75 knockdown flies. Several metabolic processes were only affected by strong ND-75 knockdown including the pentose phosphate pathway and the metabolite 2-hydroxyglutarate (2-HG), suggesting 2-HG as a candidate biomarker of severe neurological mitochondrial disease. Thus, our Drosophila model provides the means to dissect the mechanisms underlying phenotypic heterogeneity in mitochondrial disease.
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Affiliation(s)
- Lucy Granat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Debbra Y. Knorr
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Daniel C. Ranson
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Ram Prosad Chakrabarty
- Department of Medicine, Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Navdeep S. Chandel
- Department of Medicine, Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph M. Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
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Gouiza I, Hechmi M, Zioudi A, Dallali H, Kheriji N, Charif M, Le Mao M, Galai S, Kraoua L, Ben Youssef-Turki I, Kraoua I, Lenaers G, Kefi R. Expanding the genetic spectrum of mitochondrial diseases in Tunisia: novel variants revealed by whole-exome sequencing. Front Genet 2024; 14:1259826. [PMID: 38283147 PMCID: PMC10811255 DOI: 10.3389/fgene.2023.1259826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction: Inherited mitochondrial diseases are the most common group of metabolic disorders caused by a defect in oxidative phosphorylation. They are characterized by a wide clinical and genetic spectrum and can manifest at any age. In this study, we established novel phenotype-genotype correlations between the clinical and molecular features of a cohort of Tunisian patients with mitochondrial diseases. Materials and methods: Whole-exome sequencing was performed on five Tunisian patients with suspected mitochondrial diseases. Then, a combination of filtering and bioinformatics prediction tools was utilized to assess the pathogenicity of genetic variations. Sanger sequencing was subsequently performed to confirm the presence of potential deleterious variants in the patients and verify their segregation within families. Structural modeling was conducted to study the effect of novel variants on the protein structure. Results: We identified two novel homozygous variants in NDUFAF5 (c.827G>C; p.Arg276Pro) and FASTKD2 (c.496_497del; p.Leu166GlufsTer2) associated with a severe clinical form of Leigh and Leigh-like syndromes, respectively. Our results further disclosed two variants unreported in North Africa, in GFM2 (c.569G>A; p.Arg190Gln) and FOXRED1 (c.1261G>A; p.Val421Met) genes, and we described the first case of fumaric aciduria in a Tunisian patient harboring the c.1358T>C; p.Leu453Pro FH variant. Conclusion: Our study expands the mutational and phenotypic spectrum of mitochondrial diseases in Tunisia and highlights the importance of next-generation sequencing to decipher the pathomolecular mechanisms responsible for these disorders in an admixed population.
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Affiliation(s)
- Ismail Gouiza
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Abir Zioudi
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Majida Charif
- Genetics and Immuno-Cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Morgane Le Mao
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
| | - Said Galai
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Department of Clinical Biology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Lilia Kraoua
- Tunis El Manar University, Tunis, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ilhem Ben Youssef-Turki
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Ichraf Kraoua
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Guy Lenaers
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
- Department of Neurology, CHU d’Angers, Angers, France
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 DOI: 10.1038/s41580-023-00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Chen PS, Lee NC, Sung CJ, Liu YW, Weng WC, Fan PC, Lee WT, Chien YH, Wu CS, Sung YF, Tsai MC, Lee YC, Hsueh HW, Fan SMY, Wu MC, Li H, Chen HY, Lin HI, Ou-Yang CH, Hwuh WL, Lin CH. Phenotypic Heterogeneity in Patients with Mutations in the Mitochondrial Complex I Assembly Gene NDUFAF5. Mov Disord 2023; 38:2217-2229. [PMID: 37752895 DOI: 10.1002/mds.29604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Rare mutations in NADH:ubiquinone oxidoreductase complex assembly factor 5 (NDUFAF5) are linked to Leigh syndrome. OBJECTIVE We aimed to describe clinical characteristics and functional findings in a patient cohort with NDUFAF5 mutations. METHODS Patients with biallelic NDUFAF5 mutations were recruited from multi-centers in Taiwan. Clinical, laboratory, radiological, and follow-up features were recorded and mitochondrial assays were performed in patients' skin fibroblasts. RESULTS Nine patients from seven unrelated pedigrees were enrolled, eight homozygous for c.836 T > G (p.Met279Arg) in NDUFAF5 and one compound heterozygous for p.Met279Arg. Onset age had a bimodal distribution. The early-onset group (age <3 years) presented with psychomotor delay, seizure, respiratory failure, and hyponatremia. The late-onset group (age ≥5 years) presented with normal development, but slowly progressive dystonia. Combing 25 previously described patients, the p.Met279Arg variant was exclusively identified in Chinese ancestry. Compared with other groups, patients with late-onset homozygous p.Met279Arg were older at onset (P = 0.008), had less developmental delay (P = 0.01), less hyponatremia (P = 0.01), and better prognosis with preserved ambulatory function into early adulthood (P = 0.01). Bilateral basal ganglia necrosis was a common radiological feature, but brainstem and spinal cord involvement was more common with early-onset patients (P = 0.02). A modifier gene analysis showed higher concomitant mutation burden in early-versus late-onset p.Met279Arg homozygous cases (P = 0.04), consistent with more impaired mitochondrial function in fibroblasts from an early-onset case than a late-onset patient. CONCLUSIONS The p.Met279Arg variant is a common mutation in our population with phenotypic heterogeneity and divergent prognosis based on age at onset. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Pin-Shiuan Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chieh-Ju Sung
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Wen Liu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chin Weng
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Pi-Chuan Fan
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chao-Szu Wu
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Yueh-Feng Sung
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Chen Tsai
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sabrina Mai-Yi Fan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Meng-Chen Wu
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Geriatrics and Gerontology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsun Li
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Huan-Yun Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Han-I Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Hsin Ou-Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwuh
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
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12
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Viering DH, Vermeltfoort L, Bindels RJ, Deinum J, de Baaij JH. Electrolyte Disorders in Mitochondrial Cytopathies: A Systematic Review. J Am Soc Nephrol 2023; 34:1875-1888. [PMID: 37678265 PMCID: PMC10631606 DOI: 10.1681/asn.0000000000000224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
SIGNIFICANCE STATEMENT Several recent studies identified mitochondrial mutations in patients with Gitelman or Fanconi syndrome. Mitochondrial cytopathies are generally not considered in the diagnostic workup of patients with electrolyte disorders. In this systematic review, we investigated the presence of electrolyte disorders in patients with mitochondrial cytopathies to determine the relevance of mitochondrial mutation screening in this population. Our analysis demonstrates that electrolyte disorders are commonly reported in mitochondrial cytopathies, often as presenting symptoms. Consequently, more clinical attention should be raised for mitochondrial disease as cause for disturbances in electrolyte homeostasis. Further prospective cohort studies are required to determine the exact prevalence of electrolyte disorders in mitochondrial cytopathies. BACKGROUND Electrolyte reabsorption in the kidney has a high energy demand. Proximal and distal tubular epithelial cells have a high mitochondrial density for energy release. Recently, electrolyte disorders have been reported as the primary presentation of some mitochondrial cytopathies. However, the prevalence and the pathophysiology of electrolyte disturbances in mitochondrial disease are unknown. Therefore, we systematically investigated electrolyte disorders in patients with mitochondrial cytopathies. METHODS We searched PubMed, Embase, and Google Scholar for articles on genetically confirmed mitochondrial disease in patients for whom at least one electrolyte is reported. Patients with a known second genetic anomaly were excluded. We evaluated 214 case series and reports (362 patients) as well as nine observational studies. Joanna Briggs Institute criteria were used to evaluate the quality of included studies. RESULTS Of 362 reported patients, 289 had an electrolyte disorder, with it being the presenting or main symptom in 38 patients. The average number of different electrolyte abnormalities per patient ranged from 2.4 to 1.0, depending on genotype. Patients with mitochondrial DNA structural variants seemed most affected. Reported pathophysiologic mechanisms included renal tubulopathies and hormonal, gastrointestinal, and iatrogenic causes. CONCLUSIONS Mitochondrial diseases should be considered in the evaluation of unexplained electrolyte disorders. Furthermore, clinicians should be aware of electrolyte abnormalities in patients with mitochondrial disease.
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Affiliation(s)
- Daan H.H.M. Viering
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lars Vermeltfoort
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - René J.M. Bindels
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen H.F. de Baaij
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
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13
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Liu J, Lu W, Yan D, Guo J, Zhou L, Shi B, Su X. Mitochondrial respiratory complex I deficiency inhibits brown adipogenesis by limiting heme regulation of histone demethylation. Mitochondrion 2023; 72:22-32. [PMID: 37451354 DOI: 10.1016/j.mito.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Mitochondrial functions play a crucial role in determining the metabolic and thermogenic status of brown adipocytes. Increasing evidence reveals that the mitochondrial oxidative phosphorylation (OXPHOS) system plays an important role in brown adipogenesis, but the mechanistic insights are limited. Herein, we explored the potential metabolic mechanisms leading to OXPHOS regulation of brown adipogenesis in pharmacological and genetic models of mitochondrial respiratory complex I deficiency. OXPHOS deficiency inhibits brown adipogenesis through disruption of the brown adipogenic transcription circuit without affecting ATP levels. Neither blockage of calcium signaling nor antioxidant treatment can rescue the suppressed brown adipogenesis. Metabolomics analysis revealed a decrease in levels of tricarboxylic acid cycle intermediates and heme. Heme supplementation specifically enhances respiratory complex I activity without affecting complex II and partially reverses the inhibited brown adipogenesis by OXPHOS deficiency. Moreover, the regulation of brown adipogenesis by the OXPHOS-heme axis may be due to the suppressed histone methylation status by increasing histone demethylation. In summary, our findings identified a heme-sensing retrograde signaling pathway that connects mitochondrial OXPHOS to the regulation of brown adipocyte differentiation and metabolic functions.
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Affiliation(s)
- Jingjing Liu
- Department of Biochemistry and Molecular Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Wen Lu
- Department of Endocrinology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Dongyue Yan
- Department of Biochemistry and Molecular Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Junyuan Guo
- Department of Biochemistry and Molecular Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Li Zhou
- Department of Nutrition, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Bimin Shi
- Department of Endocrinology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Xiong Su
- Department of Biochemistry and Molecular Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China.
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14
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Cheng J, Li G, Wang W, Stovall DB, Sui G, Li D. Circular RNAs with protein-coding ability in oncogenesis. Biochim Biophys Acta Rev Cancer 2023; 1878:188909. [PMID: 37172651 DOI: 10.1016/j.bbcan.2023.188909] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
As ubiquitously expressed transcripts in eukaryotes, circular RNAs (circRNAs) are covalently closed and lack a 5'-cap and 3'-polyadenylation (poly (A)) tail. Initially, circRNAs were considered non-coding RNA (ncRNA), and their roles as sponging molecules to adsorb microRNAs have been extensively reported. However, in recent years, accumulating evidence has demonstrated that circRNAs could encode functional polypeptides through the initiation of translation mediated by internal ribosomal entry sites (IRESs) or N6-methyladenosine (m6A). In this review, we collectively discuss the biogenesis, cognate mRNA products, regulatory mechanisms, aberrant expression and biological phenotypes or clinical relevance of all currently reported, cancer-relevant protein-coding circRNAs. Overall, we provide a comprehensive overview of circRNA-encoded proteins and their physiological and pathological functions.
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Affiliation(s)
- Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Daniel B Stovall
- College of Arts and Sciences, Winthrop University, Rock Hill, SC 29733, United States
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
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15
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Eichwald T, da Silva LDB, Staats Pires AC, Niero L, Schnorrenberger E, Filho CC, Espíndola G, Huang WL, Guillemin GJ, Abdenur JE, Latini A. Tetrahydrobiopterin: Beyond Its Traditional Role as a Cofactor. Antioxidants (Basel) 2023; 12:1037. [PMID: 37237903 PMCID: PMC10215290 DOI: 10.3390/antiox12051037] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Tetrahydrobiopterin (BH4) is an endogenous cofactor for some enzymatic conversions of essential biomolecules, including nitric oxide, and monoamine neurotransmitters, and for the metabolism of phenylalanine and lipid esters. Over the last decade, BH4 metabolism has emerged as a promising metabolic target for negatively modulating toxic pathways that may result in cell death. Strong preclinical evidence has shown that BH4 metabolism has multiple biological roles beyond its traditional cofactor activity. We have shown that BH4 supports essential pathways, e.g., to generate energy, to enhance the antioxidant resistance of cells against stressful conditions, and to protect from sustained inflammation, among others. Therefore, BH4 should not be understood solely as an enzyme cofactor, but should instead be depicted as a cytoprotective pathway that is finely regulated by the interaction of three different metabolic pathways, thus assuring specific intracellular concentrations. Here, we bring state-of-the-art information about the dependency of mitochondrial activity upon the availability of BH4, as well as the cytoprotective pathways that are enhanced after BH4 exposure. We also bring evidence about the potential use of BH4 as a new pharmacological option for diseases in which mitochondrial disfunction has been implicated, including chronic metabolic disorders, neurodegenerative diseases, and primary mitochondriopathies.
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Affiliation(s)
- Tuany Eichwald
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
- Laboratory for Energy Metabolism, Division of Metabolic Disorders, CHOC Children’s Hospital, Orange, CA 92868, USA; (W.-L.H.); (J.E.A.)
| | - Lucila de Bortoli da Silva
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
| | - Ananda Christina Staats Pires
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
- Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Laís Niero
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
| | - Erick Schnorrenberger
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
| | - Clovis Colpani Filho
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
| | - Gisele Espíndola
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
- Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Wei-Lin Huang
- Laboratory for Energy Metabolism, Division of Metabolic Disorders, CHOC Children’s Hospital, Orange, CA 92868, USA; (W.-L.H.); (J.E.A.)
| | - Gilles J. Guillemin
- Neuroinflammation Group, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - José E. Abdenur
- Laboratory for Energy Metabolism, Division of Metabolic Disorders, CHOC Children’s Hospital, Orange, CA 92868, USA; (W.-L.H.); (J.E.A.)
| | - Alexandra Latini
- Laboratório de Bioenergética e Estresse Oxidativo—LABOX, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88037-100, SC, Brazil; (T.E.); (L.N.); (C.C.F.); (G.E.)
- Laboratory for Energy Metabolism, Division of Metabolic Disorders, CHOC Children’s Hospital, Orange, CA 92868, USA; (W.-L.H.); (J.E.A.)
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16
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Pei J, Zhang J, Cong Q. Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. Bioinformatics 2022; 38:4301-4311. [PMID: 35881696 DOI: 10.1093/bioinformatics/btac527] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein-protein interactions (PPIs) and modeling protein complexes at the proteome level. RESULTS We applied RoseTTAFold and AlphaFold, two of the latest deep-learning methods for structure predictions, to analyze coevolution of human proteins residing in mitochondria, an organelle of vital importance in many cellular processes including energy production, metabolism, cell death and antiviral response. Variations in mitochondrial proteins have been linked to a plethora of human diseases and genetic conditions. RoseTTAFold, with high computational speed, was used to predict the coevolution of about 95% of mitochondrial protein pairs. Top-ranked pairs were further subject to modeling of the complex structures by AlphaFold, which also produced contact probability with high precision and in many cases consistent with RoseTTAFold. Most top-ranked pairs with high contact probability were supported by known PPIs and/or similarities to experimental structural complexes. For high-scoring pairs without experimental complex structures, our coevolution analyses and structural models shed light on the details of their interfaces, including CHCHD4-AIFM1, MTERF3-TRUB2, FMC1-ATPAF2 and ECSIT-NDUFAF1. We also identified novel PPIs (PYURF-NDUFAF5, LYRM1-MTRF1L and COA8-COX10) for several proteins without experimentally characterized interaction partners, leading to predictions of their molecular functions and the biological processes they are involved in. AVAILABILITY AND IMPLEMENTATION Data of mitochondrial proteins and their interactions are available at: http://conglab.swmed.edu/mitochondria. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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17
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Demarest S, Calhoun J, Eschbach K, Yu HC, Mirsky D, Angione K, Shaikh TH, Carvill GL, Benke TA, Gunti J, Vanderveen G. Whole-exome sequencing and adrenocorticotropic hormone therapy in individuals with infantile spasms. Dev Med Child Neurol 2022; 64:633-640. [PMID: 35830182 DOI: 10.1111/dmcn.15109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022]
Abstract
AIM To identify additional genes associated with infantile spasms using a cohort with defined infantile spasms. METHOD Whole-exome sequencing (WES) was performed on 21 consented individuals with infantile spasms and their unaffected parents (a trio-based study). Clinical history and imaging were reviewed. Potentially deleterious exonic variants were identified and segregated. To refine potential candidates, variants were further prioritized on the basis of evidence for relevance to disease phenotype or known associations with infantile spasms, epilepsy, or neurological disease. RESULTS Likely pathogenic de novo variants were identified in NR2F1, GNB1, NEUROD2, GABRA2, and NDUFAF5. Suggestive dominant and recessive candidate variants were identified in PEMT, DYNC1I1, ASXL1, RALGAPB, and STRADA; further confirmation is required to support their relevance to disease etiology. INTERPRETATION This study supports the utility of WES in uncovering the genetic etiology in undiagnosed individuals with infantile spasms with an overall yield of five out of 21. High-priority candidates were identified in an additional five individuals. WES provides additional support for previously described disease-associated genes and expands their already broad mutational and phenotypic spectrum.
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Affiliation(s)
- Scott Demarest
- Children's Hospital Colorado, Aurora, CO, USA.,Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Jeff Calhoun
- Ken and Ruth Davee Department of Neurology, Northwestern University, School of Medicine, Chicago, IL, USA
| | - Krista Eschbach
- Children's Hospital Colorado, Aurora, CO, USA.,Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Hung-Chun Yu
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - David Mirsky
- Children's Hospital Colorado, Aurora, CO, USA.,Department of Radiology, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Katie Angione
- Children's Hospital Colorado, Aurora, CO, USA.,Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Tamim H Shaikh
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University, School of Medicine, Chicago, IL, USA.,Department of Pharmacology, Northwestern University, School of Medicine, Chicago, IL, USA.,Department of Pediatrics, Northwestern University, School of Medicine, Chicago, IL, USA
| | - Tim A Benke
- Children's Hospital Colorado, Aurora, CO, USA.,Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO, USA.,Department of Pharmacology, University of Colorado, School of Medicine, Aurora, CO, USA.,Department of Neurology, University of Colorado, School of Medicine, Aurora, CO, USA.,Department of Otolaryngology, University of Colorado, School of Medicine, Aurora, CO, USA
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18
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Yépez VA, Gusic M, Kopajtich R, Mertes C, Smith NH, Alston CL, Ban R, Beblo S, Berutti R, Blessing H, Ciara E, Distelmaier F, Freisinger P, Häberle J, Hayflick SJ, Hempel M, Itkis YS, Kishita Y, Klopstock T, Krylova TD, Lamperti C, Lenz D, Makowski C, Mosegaard S, Müller MF, Muñoz-Pujol G, Nadel A, Ohtake A, Okazaki Y, Procopio E, Schwarzmayr T, Smet J, Staufner C, Stenton SL, Strom TM, Terrile C, Tort F, Van Coster R, Vanlander A, Wagner M, Xu M, Fang F, Ghezzi D, Mayr JA, Piekutowska-Abramczuk D, Ribes A, Rötig A, Taylor RW, Wortmann SB, Murayama K, Meitinger T, Gagneur J, Prokisch H. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Med 2022; 14:38. [PMID: 35379322 PMCID: PMC8981716 DOI: 10.1186/s13073-022-01019-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
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Affiliation(s)
- Vicente A. Yépez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Mertes
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Nicholas H. Smith
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Rui Ban
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Center for Pediatric Research Leipzig (CPL), Center for Rare Diseases, University Hospitals, University of Leipzig, Leipzig, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Blessing
- Department for Inborn Metabolic Diseases, Children’s and Adolescents’ Hospital, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Elżbieta Ciara
- Department of Medical Genetics, Children’s Memorial Health Institute, Warsaw, Poland
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, Reutlingen, Germany
| | - Johannes Häberle
- University Children’s Hospital Zurich and Children’s Research Centre, Zürich, Switzerland
| | - Susan J. Hayflick
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
| | - Dominic Lenz
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Makowski
- Department of Pediatrics, Technical University of Munich, Munich, Germany
| | - Signe Mosegaard
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michaela F. Müller
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnieszka Nadel
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Elena Procopio
- Inborn Metabolic and Muscular Disorders Unit, Anna Meyer Children Hospital, Florence, Italy
| | - Thomas Schwarzmayr
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Christian Staufner
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah L. Stenton
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M. Strom
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caterina Terrile
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manting Xu
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Fang
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnès Rötig
- Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Saskia B. Wortmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc Nijmegen, Nijmegen, The Netherlands
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Chiba, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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19
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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20
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Wen Y, Lu G, Qiao L, Li Y. A Leigh syndrome caused by compound heterozygous mutations on NDUFAF5 induce early infant death: A case report. Mol Genet Genomic Med 2021; 10:e1852. [PMID: 34964562 PMCID: PMC8801144 DOI: 10.1002/mgg3.1852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 01/25/2023] Open
Abstract
Background The NADH:ubiquinone oxidoreductase complex assembly factor gene (NDUFAF5) has been linked to the occurrence of Leigh syndrome, but few causative mutations have been identified. Here we report a rare case of Leigh syndrome in an infant who died in the early postnatal period. Methods We performed whole‐exome sequencing (WES) and mutation analysis of NDUFAF5 to obtain genetic data on the patient and describe the clinical and genetic characteristics. Results The proband was a 2‐month‐old male infant who suffered from recurrent vomiting and persistent seizure and died at 2 months of age after early medical support and treatment. His parents reported the unexplained death of the infant's older brother at 1 year of age. WES of the patient's DNA revealed c.357C>G and c.611C>T compound heterozygous mutations in NDUFAF5; analysis with the MutationTaster application indicated that both were pathogenic (p = 0.99). Significant structural changes in the transport domain of the protein were predicted using SWISS‐MODEL. We estimated the stability of the mutant protein using a mutation cutoff scanning matrix and found reductions in Gibbs free energy (−0.623 kcal/mol for p.D119E and −0.813 kcal/mol for p.A204V), indicating that the mutations led to an unstable protein structure. We speculated that the patient died as a result of impaired mitochondrial function caused by the NDUFAF5 mutations, and made a diagnosis of Leigh syndrome. Conclusion Our results demonstrate that molecular genetic screening is useful for the diagnosis of mitochondrial diseases, especially in children with a positive family history. Leigh syndrome should be considered in the diagnosis of patients presenting with severe recurrent vomiting and feeding difficulties with persistent seizure. Our findings expand the mutation spectrum of the NDUFAF5 gene and contribute to the genotype–phenotype map of mitochondrial respiratory chain complex I deficiency.
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Affiliation(s)
- Yan Wen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Emergency, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Guoyan Lu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lina Qiao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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21
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Bi H, Guo H, Wang Q, Zhang X, Zhao Y, Li J, Zhao W, Tuo H, Zhang Y. Corrigendum: A Novel Variation in the Mitochondrial Complex I Assembly Factor NDUFAF5 Causes Isolated Bilateral Striatal Necrosis in Childhood. Front Neurol 2021; 12:792230. [PMID: 34858319 PMCID: PMC8630781 DOI: 10.3389/fneur.2021.792230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Hongyan Bi
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Qianfei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiao Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yaming Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jimei Li
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weiqin Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Houzhen Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongbo Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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22
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Legro NR, Kumar A, Aliu E. Case report of atypical Leigh syndrome in an adolescent male with novel biallelic variants in NDUFAF5 and review of the natural history of NDUFAF5-related disorders. Am J Med Genet A 2021; 188:896-899. [PMID: 34797029 DOI: 10.1002/ajmg.a.62568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
NDUFAF5 encodes a Complex I assembly factor which is critical to the modification of a core subunit, NDUFS7, in early Complex I factor assembly. Mutations in NDUFAF5 have been previously shown to cause Complex I deficiency leading to mitochondrial respiratory chain impairment. More than 15 individuals affected by variants in NDUFAF5 have been described; however, there is phenotypic heterogeneity within this cohort. Some individuals display features of classical Leigh syndrome with early onset neurodegeneration whereas others live into early adulthood with progressive neurological deficits. Here, we present a clinical report of a 17-year-old African American individual with compound heterozygous mutations in NDUFAF5. The individual presented with childhood onset bilateral optic atrophy and developed progressive neuromuscular decline with relatively preserved cognition over time.
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Affiliation(s)
- Nicole R Legro
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.,Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Ashutosh Kumar
- Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.,Division of Neurology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ermal Aliu
- Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.,Division of Medical Genetics, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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23
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Bi H, Guo H, Wang Q, Zhang X, Zhao Y, Li J, Zhao W, Tuo H, Zhang Y. A Novel Variation in the Mitochondrial Complex I Assembly Factor NDUFAF5 Causes Isolated Bilateral Striatal Necrosis in Childhood. Front Neurol 2021; 12:675616. [PMID: 34177781 PMCID: PMC8223072 DOI: 10.3389/fneur.2021.675616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 01/30/2023] Open
Abstract
Background: Bilateral striatal necrosis (BSN) is characterized by symmetrical degeneration, predominantly of the caudate and putamen nucleus, in the basal ganglia. It is associated with numerous acquired and hereditary neuro-developmental and motor dysfunction-related pathological conditions. BSN results in high morbidity and mortality among infants and children, and its diagnosis is clinically challenging due to several overlapping disease phenotypes. Therefore, a precise genetic diagnosis is urgently needed for accurate genetic counseling and improved prognostic outcomes as well. Objective: To identify novel missense mutations in the NDUFAF5 gene as a cause of childhood BSN in members of a Chinese family and summarize the clinical characteristics of patients with the NDUFAF5 gene mutations. Methods: This study included a large family living in a remote northwestern area of China. Three siblings developed a neurological disorder characterized by generalized dystonia within the first decade of their lives. Cerebral computed tomography (CT) and magnetic resonance imaging (MRI) showed bilateral lesions of the putamen. Biochemical and genetic approaches were used to identify the cause of BSN. Results: Sequence analysis showed no pathogenic variation in PANK2, SLC25A19, SLC19A3, and NUP62 genes and in the entire mitochondrial genome as well. Whole-exome sequencing revealed compound heterozygous mutations consisting of NDUFAF5:c.425A > C(p.E142A) and c.836T > G (p.M279R). The father, a healthy sister, and a healthy brother of the affected siblings carried the c.836T > G mutation, and the mother carried the c.425A > C mutation. These variants were absent in 100 ethnically matched non-BSN controls. In silico analysis demonstrated that the E142A and M279R mutations in NDUFAF5 protein significantly perturbed the normal conformation of the protein due to alterations in the hydrogen bonding patterns around the evolutionarily conserved catalytic domains, leading to its loss of function in the early stage of mitochondrial complex I assembly. Conclusions: We identified a novel compound heterozygous mutation (c.425A > C and c.836T > G) in the NDUFAF5 gene as the potential cause of autosomal recessive childhood BSN, which extended the pathogenic variation spectrum of the NDUFAF5 gene. This study provides substantial evidence for further improvement of genetic counseling and better clinical management of BSN affected individuals.
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Affiliation(s)
- Hongyan Bi
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Qianfei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yaming Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jimei Li
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weiqin Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Houzhen Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongbo Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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24
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Alston CL, Stenton SL, Hudson G, Prokisch H, Taylor RW. The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines. J Pathol 2021; 254:430-442. [PMID: 33586140 PMCID: PMC8600955 DOI: 10.1002/path.5641] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
Mitochondria play essential roles in numerous metabolic pathways including the synthesis of adenosine triphosphate through oxidative phosphorylation. Clinically, mitochondrial diseases occur when there is mitochondrial dysfunction – manifesting at any age and affecting any organ system; tissues with high energy requirements, such as muscle and the brain, are often affected. The clinical heterogeneity is parallel to the degree of genetic heterogeneity associated with mitochondrial dysfunction. Around 10% of human genes are predicted to have a mitochondrial function, and defects in over 300 genes are reported to cause mitochondrial disease. Some involve the mitochondrial genome (mtDNA), but the vast majority occur within the nuclear genome. Except for a few specific genetic defects, there remains no cure for mitochondrial diseases, which means that a genetic diagnosis is imperative for genetic counselling and the provision of reproductive options for at‐risk families. Next‐generation sequencing strategies, particularly exome and whole‐genome sequencing, have revolutionised mitochondrial diagnostics such that the traditional muscle biopsy has largely been replaced with a minimally‐invasive blood sample for an unbiased approach to genetic diagnosis. Where these genomic approaches have not identified a causative defect, or where there is insufficient support for pathogenicity, additional functional investigations are required. The application of supplementary ‘omics’ technologies, including transcriptomics, proteomics, and metabolomics, has the potential to greatly improve diagnostic strategies. This review aims to demonstrate that whilst a molecular diagnosis can be achieved for many cases through next‐generation sequencing of blood DNA, the use of patient tissues and an integrated, multidisciplinary multi‐omics approach is pivotal for the diagnosis of more challenging cases. Moreover, the analysis of clinically relevant tissues from affected individuals remains crucial for understanding the molecular mechanisms underlying mitochondrial pathology. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah L Stenton
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - 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 Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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25
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Torraco A, Nasca A, Verrigni D, Pennisi A, Zaki MS, Olivieri G, Assouline Z, Martinelli D, Maroofian R, Rizza T, Di Nottia M, Invernizzi F, Lamantea E, Longo D, Houlden H, Prokisch H, Rötig A, Dionisi-Vici C, Bertini E, Ghezzi D, Carrozzo R, Diodato D. Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation. Hum Mutat 2021; 42:699-710. [PMID: 33715266 DOI: 10.1002/humu.24195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
Isolated biochemical deficiency of mitochondrial complex I is the most frequent signature among mitochondrial diseases and is associated with a wide variety of clinical symptoms. Leigh syndrome represents the most frequent neuroradiological finding in patients with complex I defect and more than 80 monogenic causes have been involved in the disease. In this report, we describe seven patients from four unrelated families harboring novel NDUFA12 variants, with six of them presenting with Leigh syndrome. Molecular genetic characterization was performed using next-generation sequencing combined with the Sanger method. Biochemical and protein studies were achieved by enzymatic activities, blue native gel electrophoresis, and western blot analysis. All patients displayed novel homozygous mutations in the NDUFA12 gene, leading to the virtual absence of the corresponding protein. Surprisingly, despite the fact that in none of the analyzed patients, NDUFA12 protein was detected, they present a different onset and clinical course of the disease. Our report expands the array of genetic alterations in NDUFA12 and underlines phenotype variability associated with NDUFA12 defect.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessia Nasca
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Pennisi
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Giorgia Olivieri
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Zahra Assouline
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Diego Martinelli
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Teresa Rizza
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Invernizzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Longo
- Department of Diagnostic Imaging, Unit of Neuroradiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Agnès Rötig
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Carlo Dionisi-Vici
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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26
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Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J 2021; 477:4085-4132. [PMID: 33151299 PMCID: PMC7657662 DOI: 10.1042/bcj20190767] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
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27
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Wang L, Huang Y, Liu C, Guo M, Ma Z, He J, Wang A, Sun X, Liu Z. Deltex3 inhibits Epithelial Mesenchymal Transition in Papillary Thyroid Carcinoma via promoting ubiquitination of XRCC5 to regulate the AKT signal pathway. J Cancer 2021; 12:860-873. [PMID: 33403043 PMCID: PMC7778541 DOI: 10.7150/jca.48141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023] Open
Abstract
Background: Papillary thyroid carcinoma (PTC) is one of the most common endocrine malignant tumors. Poor prognoses such as high recurrence rate always appear in PTC patients with cervical lymph node metastasis. The process of ubiquitination plays important roles in PTC. As ubiquitin E3 ligases, Deltex (DTX) family proteins were reported to associate with multiple cancers. However, functions and mechanisms of DTX3 in PTC are currently unknown. Methods: In this study, DTX3 expressions were examined in 114 PTC and paired paracancerous normal tissues through quantitative real-time polymerase chain reaction and western blot. The clinical significances of DTX3 expressions in PTC patients were also investigated. After stable transfection with either short hairpin RNA to knock down DTX3 expression or full-length complementary DNA to upregulate DTX3 expression, changes of malignant phenotypes in two PTC cell lines K1 and TPC-1 were observed using cell viability, flow cytometry, wound healing and transwell assays. Afterwards, altered expressions of epithelial-mesenchymal transition (EMT) and AKT signal pathway related proteins were measured by western blot. Immunoprecipitation and mass spectrometry (IP-MS), immunofluorescence and Co-IP were utilized to identify the possible DTX3 interacting proteins. Results: Both mRNA and protein expressions of DTX3 were lower in PTC tissues and correlated with the presence of cervical lymph node metastasis (P<0.05). DTX3 overexpression inhibited migration and invasion of PTC cells, decreased Vimentin and phosphorylated AKT expressions, but promoted E-cadherin expression (P<0.05). Moreover, knockdown of DTX3 led to opposite changes (P<0.05). Total 46 probable DTX3 interacting proteins were identified by IP-MS. Among them, X-ray repair cross-complementing protein 5 (XRCC5) and NADH: Ubiquinone Oxidoreductase Complex Assembly Factor 5 (NDUFAF5) were verified to be associated with DTX3. Moreover, DTX3 was proved to be co-localized with XRCC5 in nucleus and promote ubiquitination of XRCC5. Conclusions: DTX3 suppresses EMT by partially facilitating ubiquitination of XRCC5 to inhibit AKT signal pathway in PTC.
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Affiliation(s)
- Lidong Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yonglian Huang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chenxi Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mingyue Guo
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhennan Ma
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jingni He
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ailian Wang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaodan Sun
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Ugarteburu O, Teresa Garcia-Silva M, Aldamiz-Echevarria L, Gort L, Garcia-Villoria J, Tort F, Ribes A. Complex I deficiency, due to NDUFAF4 mutations, causes severe mitochondrial dysfunction and is associated to early death and dysmorphia. Mitochondrion 2020; 55:78-84. [DOI: 10.1016/j.mito.2020.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 12/28/2022]
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Tort F, Barredo E, Parthasarathy R, Ugarteburu O, Ferrer-Cortès X, García-Villoria J, Gort L, González-Quintana A, Martín MA, Fernández-Vizarra E, Zeviani M, Ribes A. Biallelic mutations in NDUFA8 cause complex I deficiency in two siblings with favorable clinical evolution. Mol Genet Metab 2020; 131:349-357. [PMID: 33153867 DOI: 10.1016/j.ymgme.2020.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023]
Abstract
Isolated complex I (CI) deficiency is the most common cause of oxidative phosphorylation (OXPHOS) dysfunction. Whole-exome sequencing identified biallelic mutations in NDUFA8 (c.[293G > T]; [293G > T], encoding for an accessory subunit of CI, in two siblings with a favorable clinical evolution. The individuals reported here are practically asymptomatic, with the exception of slight failure to thrive and some language difficulties at the age of 6 and 9 years, respectively. These observations are remarkable since the vast majority of patients with CI deficiency, including the only NDUFA8 patient reported so far, showed an extremely poor clinical outcome. Western blot studies demonstrated that NDUFA8 protein was strongly reduced in the patients' fibroblasts and muscle extracts. In addition, there was a marked and specific decrease in the steady-state levels of CI subunits. BN-PAGE demonstrated an isolated defect in the assembly and the activity of CI with impaired supercomplexes formation and abnormal accumulation of CI subassemblies. Confocal microscopy analysis in fibroblasts showed rounder mitochondria and diminished branching degree of the mitochondrial network. Functional complementation studies demonstrated disease-causality for the identified mutation as lentiviral transduction with wild-type NDUFA8 cDNA restored the steady-state levels of CI subunits and completely recovered the deficient enzymatic activity in immortalized mutant fibroblasts. In summary, we provide additional evidence of the involvement of NDUFA8 as a mitochondrial disease-causing gene associated with altered mitochondrial morphology, CI deficiency, impaired supercomplexes formation, and very mild progression of the disease.
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Affiliation(s)
- Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | | | | | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Xenia Ferrer-Cortès
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Laura Gort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Adrián González-Quintana
- Laboratorio de Enfermedades Mitocondriales, Servicio de Bioquímica, Instituto de Investigación Hospital, 12 de Octubre (imas12), CIBERER, Madrid, Spain
| | - Miguel A Martín
- Laboratorio de Enfermedades Mitocondriales, Servicio de Bioquímica, Instituto de Investigación Hospital, 12 de Octubre (imas12), CIBERER, Madrid, Spain
| | | | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain.
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30
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Mansukhani SA, Mehta DG, Renaud DL, Whealy MA, Chen JJ, Bhatti MT. Nuclear DNA Mutation Causing a Phenotypic Leber Hereditary Optic Neuropathy Plus. Ophthalmology 2020; 128:628-631. [PMID: 32918965 DOI: 10.1016/j.ophtha.2020.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022] Open
Affiliation(s)
- Sasha A Mansukhani
- Department of Ophthalmology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Dev G Mehta
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Deborah L Renaud
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota; Department of Pediatrics, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Mark A Whealy
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - John J Chen
- Department of Ophthalmology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota; Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - M Tariq Bhatti
- Department of Ophthalmology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota; Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
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31
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Kimonis V, Al Dubaisi R, Maclean AE, Hall K, Weiss L, Stover AE, Schwartz PH, Berg B, Cheng C, Parikh S, Conner BR, Wu S, Hasso AN, Scott DA, Koenig MK, Karam R, Tang S, Smith M, Chao E, Balk J, Hatchwell E, Eis PS. NUBPL mitochondrial disease: new patients and review of the genetic and clinical spectrum. J Med Genet 2020; 58:314-325. [PMID: 32518176 DOI: 10.1136/jmedgenet-2020-106846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The nucleotide binding protein-like (NUBPL) gene was first reported as a cause of mitochondrial complex I deficiency (MIM 613621, 618242) in 2010. To date, only eight patients have been reported with this mitochondrial disorder. Five other patients were recently reported to have NUBPL disease but their clinical picture was different from the first eight patients. Here, we report clinical and genetic findings in five additional patients (four families). METHODS Whole exome sequencing was used to identify patients with compound heterozygous NUBPL variants. Functional studies included RNA-Seq transcript analyses, missense variant biochemical analyses in a yeast model (Yarrowia lipolytica) and mitochondrial respiration experiments on patient fibroblasts. RESULTS The previously reported c.815-27T>C branch-site mutation was found in all four families. In prior patients, c.166G>A [p.G56R] was always found in cis with c.815-27T>C, but only two of four families had both variants. The second variant found in trans with c.815-27T>C in each family was: c.311T>C [p.L104P] in three patients, c.693+1G>A in one patient and c.545T>C [p.V182A] in one patient. Complex I function in the yeast model was impacted by p.L104P but not p.V182A. Clinical features include onset of neurological symptoms at 3-18 months, global developmental delay, cerebellar dysfunction (including ataxia, dysarthria, nystagmus and tremor) and spasticity. Brain MRI showed cerebellar atrophy. Mitochondrial function studies on patient fibroblasts showed significantly reduced spare respiratory capacity. CONCLUSION We report on five new patients with NUBPL disease, adding to the number and phenotypic variability of patients diagnosed worldwide, and review prior reported patients with pathogenic NUBPL variants.
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Affiliation(s)
- Virginia Kimonis
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Rehab Al Dubaisi
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Andrew E Maclean
- Department of Biological Chemistry, John Innes Centre, Norwich, Norfolk, UK.,Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, Glasgow, UK
| | - Kathy Hall
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Lan Weiss
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Alexander E Stover
- CHOC National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, California, USA
| | - Philip H Schwartz
- CHOC National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, California, USA
| | - Bethany Berg
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Cheng Cheng
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Sumit Parikh
- Center for Pediatric Neurology, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Sitao Wu
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Anton N Hasso
- Radiological Sciences, University of California Irvine School of Medicine, Irvine, California, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Mary Kay Koenig
- Department of Pediatrics, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Rachid Karam
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Sha Tang
- Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Moyra Smith
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA
| | - Elizabeth Chao
- Division of Genetics and Metabolism, Department of Pediatrics, University of California Irvine, Irvine, California, USA.,Ambry Genetics Corp, Aliso Viejo, California, USA
| | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich, Norfolk, UK
| | | | - Peggy S Eis
- Population Bio, Inc, New York, New York, USA
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32
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Mukherjee S, Ghosh A. Molecular mechanism of mitochondrial respiratory chain assembly and its relation to mitochondrial diseases. Mitochondrion 2020; 53:1-20. [PMID: 32304865 DOI: 10.1016/j.mito.2020.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/28/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022]
Abstract
The mitochondrial respiratory chain (MRC) is comprised of ~92 nuclear and mitochondrial DNA-encoded protein subunits that are organized into five different multi-subunit respiratory complexes. These complexes produce 90% of the ATP required for cell sustenance. Specific sets of subunits are assembled in a modular or non-modular fashion to construct the MRC complexes. The complete assembly process is gradually chaperoned by a myriad of assembly factors that must coordinate with several other prosthetic groups to reach maturity, makingthe entire processextensively complicated. Further, the individual respiratory complexes can be integrated intovarious giant super-complexes whose functional roles have yet to be explored. Mutations in the MRC subunits and in the related assembly factors often give rise to defects in the proper assembly of the respiratory chain, which then manifests as a group of disorders called mitochondrial diseases, the most common inborn errors of metabolism. This review summarizes the current understanding of the biogenesis of individual MRC complexes and super-complexes, and explores how mutations in the different subunits and assembly factors contribute to mitochondrial disease pathology.
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Affiliation(s)
- Soumyajit Mukherjee
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India.
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33
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Alston CL, Veling MT, Heidler J, Taylor LS, Alaimo JT, Sung AY, He L, Hopton S, Broomfield A, Pavaine J, Diaz J, Leon E, Wolf P, McFarland R, Prokisch H, Wortmann SB, Bonnen PE, Wittig I, Pagliarini DJ, Taylor RW. Pathogenic Bi-allelic Mutations in NDUFAF8 Cause Leigh Syndrome with an Isolated Complex I Deficiency. Am J Hum Genet 2020; 106:92-101. [PMID: 31866046 PMCID: PMC7042492 DOI: 10.1016/j.ajhg.2019.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022] Open
Abstract
Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. It is characterized by symmetrical lesions found on neuroimaging in the basal ganglia, thalamus, and brainstem and by a loss of motor skills and delayed developmental milestones. Genetic diagnosis of Leigh syndrome is complicated on account of the vast genetic heterogeneity with >75 candidate disease-associated genes having been reported to date. Candidate genes are still emerging, being identified when “omics” tools (genomics, proteomics, and transcriptomics) are applied to manipulated cell lines and cohorts of clinically characterized individuals who lack a genetic diagnosis. NDUFAF8 is one such protein; it has been found to interact with the well-characterized complex I (CI) assembly factor NDUFAF5 in a large-scale protein-protein interaction screen. Diagnostic next-generation sequencing has identified three unrelated pediatric subjects, each with a clinical diagnosis of Leigh syndrome, who harbor bi-allelic pathogenic variants in NDUFAF8. These variants include a recurrent splicing variant that was initially overlooked due to its deep-intronic location. Subject fibroblasts were found to express a complex I deficiency, and lentiviral transduction with wild-type NDUFAF8-cDNA ameliorated both the assembly defect and the biochemical deficiency. Complexome profiling of subject fibroblasts demonstrated a complex I assembly defect, and the stalled assembly intermediates corroborate the role of NDUFAF8 in early complex I assembly. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and to validate the clinical utility of orphan protein characterization. We also highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.
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Barbosa-Gouveia S, González-Vioque E, Borges F, Gutiérrez-Solana L, Wintjes L, Kappen A, van den Heuvel L, Leis R, Rodenburg R, Couce ML. Identification and Characterization of New Variants in FOXRED1 Gene Expands the Clinical Spectrum Associated with Mitochondrial Complex I Deficiency. J Clin Med 2019; 8:jcm8081262. [PMID: 31434271 PMCID: PMC6723710 DOI: 10.3390/jcm8081262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 11/16/2022] Open
Abstract
Complex I (nicotinamide adenine dinucleotide (NADH): ubiquinone oxidoreductase) is the largest complex of the mitochondrial oxidative phosphorylation system (OXPHOS) system. Forty-four subunits encoded in nuclear and mitochondrial genomes compose this multiprotein complex, its assembly being a highly complex process involving at least 15 additional nuclear encoded assembly factors. Complex I deficiency is a mitochondrial disorder usually associated with early-onset severe multisystem disorders characterized by highly variable clinical manifestations. Flavin adenine dinucleotide (FAD)-dependent oxidoreductase domain-containing protein 1 (FOXRED1) is a complex I assembly factor. To date, only five patients with mitochondrial complex I deficiency due to mutations in FOXRED1 have been characterized. Here, we describe a child with ataxia, epilepsy and psychomotor developmental delay carrying two heterozygous FOXRED1 variants, c.920G>A (p.Gly307Glu) and c.733+1G>A. We demonstrate the molecular mechanism supporting the pathogenicity of the FOXRED1 variants, showing a clear deficiency of complex I activity. The reduction in the steady-state level of complex I holoenzyme in patient fibroblasts, confirmed the pathogenicity of the variants and showed the molecular mechanism behind their pathogenicity. A comparison of the clinical presentation of the index case with the previously described cases allowed deepening our knowledge about the clinical variability associated with FOXRED1 defects.
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Affiliation(s)
- Sofia Barbosa-Gouveia
- Diagnosis and Treatment of Congenital Metabolic Diseases Unit (UDyTEMC), Department of Pediatrics, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain.
- Faculty of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain.
- IDIS-Health Research Institute of Santiago de Compostela, 15706 Santiago de Compostela, Spain.
| | - Emiliano González-Vioque
- Diagnosis and Treatment of Congenital Metabolic Diseases Unit (UDyTEMC), Department of Pediatrics, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain
- IDIS-Health Research Institute of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Filipa Borges
- Diagnosis and Treatment of Congenital Metabolic Diseases Unit (UDyTEMC), Department of Pediatrics, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Luis Gutiérrez-Solana
- Unit of Child Neurology, Department of Pediatrics, Hospital Infantil Universitario Niño Jesús de Madrid, 28009 Madrid, Spain
| | - Liesbeth Wintjes
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Antonia Kappen
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Lambert van den Heuvel
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Rosaura Leis
- IDIS-Health Research Institute of Santiago de Compostela, 15706 Santiago de Compostela, Spain
- Unit of Pediatric Gastroenterology and Nutrition Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
- CIBER Fisiopatología Obesidad y Nutrición (CIBEROBN), Instituto Salud Carlos III, 28029 Madrid, Spain
| | - Richard Rodenburg
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - María Luz Couce
- Diagnosis and Treatment of Congenital Metabolic Diseases Unit (UDyTEMC), Department of Pediatrics, Clinical University Hospital of Santiago de Compostela, 15706 Santiago de Compostela, Spain
- Faculty of Medicine, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
- IDIS-Health Research Institute of Santiago de Compostela, 15706 Santiago de Compostela, Spain
- CIBERER, Pabellón 11, 28029 Madrid, Spain
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35
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Finsterer J. NDUFAF5 variants manifest phenotypically heterogeneously. Mol Genet Metab Rep 2018; 18:8-9. [PMID: 30581749 PMCID: PMC6293042 DOI: 10.1016/j.ymgmr.2018.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 11/28/2022] Open
Affiliation(s)
- Josef Finsterer
- Krankenanstalt Rudolfstiftung, Messerli Institute, Veterinary University of Vienna, Vienna, Austria
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