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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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Crooks DR, Cawthon GM, Fitzsimmons CM, Perez M, Ricketts CJ, Vocke CD, Yang Y, Middelton L, Nielsen D, Schmidt LS, Tandon M, Merino MJ, Ball MW, Meier JL, Batista PJ, Linehan WM. Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer. Hum Mol Genet 2023; 32:3135-3145. [PMID: 37561409 PMCID: PMC10630246 DOI: 10.1093/hmg/ddad131] [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: 07/07/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is an autosomal dominant condition characterized by the development of cutaneous and uterine leiomyomas and risk for development of an aggressive form of papillary renal cell cancer. HLRCC is caused by germline inactivating pathogenic variants in the fumarate hydratase (FH) gene, which encodes the enzyme that catalyzes the interconversion of fumarate and L-malate. We utilized enzyme and protein mobility assays to evaluate the FH enzyme in a cohort of patients who showed clinical manifestations of HLRCC but were negative for known pathogenic FH gene variants. FH enzyme activity and protein levels were decreased by 50% or greater in three family members, despite normal FH mRNA expression levels as measured by quantitative PCR. Direct Nanopore RNA sequencing demonstrated 57 base pairs of retained intron sequence between exons 9 and 10 of polyadenylated FH mRNA in these patients, resulting in a truncated FH protein. Genomic sequencing revealed a heterozygous intronic alteration of the FH gene (chr1: 241498239 T/C) resulting in formation of a splice acceptor site near a polypyrimidine tract, and a uterine fibroid obtained from a patient showed loss of heterozygosity at this site. The same intronic FH variant was identified in an unrelated patient who also showed a clinical phenotype of HLRCC. These data demonstrate that careful clinical assessment as well as biochemical characterization of FH enzyme activity, protein expression, direct RNA sequencing, and genomic DNA sequencing of patient-derived cells can identify pathogenic variants outside of the protein coding regions of the FH gene.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Geetha Mariah Cawthon
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Christina M Fitzsimmons
- RNA Metabolism and Epitranscriptomics Unit, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Minervo Perez
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyles St., Frederick, MD 21072, United States
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Lindsay Middelton
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Debbie Nielsen
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, 1050 Boyles St. Frederick, MD 21701, United States
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource (CCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., 1050 Boyles St., Frederick, MD 21072, United States
| | - Maria J Merino
- Translational Surgical Pathology, Laboratory of Pathology Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyles St., Frederick, MD 21072, United States
| | - Pedro J Batista
- RNA Metabolism and Epitranscriptomics Unit, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - William Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
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Reis‐Carneiro D, Robalo C, Laço M, Vidailhet M, Diogo L. Progressive Generalized Dystonia‐Parkinsonism in a Child with Fumaric Aciduria. Mov Disord Clin Pract 2022; 9:707-709. [PMID: 35844283 PMCID: PMC9274347 DOI: 10.1002/mdc3.13450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Diogo Reis‐Carneiro
- Neurology Department Centro Hospitalar e Universitário de Coimbra Coimbra Portugal
| | - Conceição Robalo
- Neuropediatrics Department Centro Hospitalar e Universitário de Coimbra Coimbra Portugal
| | - Mário Laço
- Medical Genetics Unit, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra Coimbra Portugal
| | - Marie Vidailhet
- Neurology Department Hôpital de la Salpêtrière, AP‐HP Paris France
- Institut du Cerveau‐Paris Brain Institute‐ICM, Inserm U1127, CNRS UMR 7225 Sorbonne Université Paris France
| | - Luísa Diogo
- Reference Centre for Inherited Metabolic Disorders—Centro Hospitalar e Universitário de Coimbra Coimbra Portugal
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