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Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
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Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
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2
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Delibes C, Ferré M, Rozet M, Desquiret-Dumas V, Descatha A, Gohier B, Gohier P, Amati-Bonneau P, Milea D, Reynier P. Genetic susceptibility to optic neuropathy in patients with alcohol use disorder. J Transl Med 2024; 22:495. [PMID: 38796496 PMCID: PMC11127293 DOI: 10.1186/s12967-024-05334-0] [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: 02/27/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND The pathophysiology of toxico-nutritional optic neuropathies remains debated, with no clear understanding of the respective roles played by the direct alcohol toxicity, smoking and the often associated vitamin deficiencies, which are risk factors for optic neuropathy. Our aim was to investigate genetic susceptibility in patients with bilateral infraclinical optic neuropathy associated with chronic alcohol use disorder. METHODS This retrospective cohort study included 102 visually asymptomatic patients with documented alcohol use disorder from a French reference center. Optic neuropathy was identified with optical coherence tomography (OCT), after which genetic susceptibility in the group of affected patients was investigated. Genetic testing was performed using panel sequencing of 87 nuclear genes and complete mitochondrial DNA sequencing. RESULTS Optic neuropathy was detected in 36% (37/102) of the included patients. Genetic testing of affected patients disclosed two patients (2/30, 6.7%) with optic neuropathy associated with pathogenic variants affecting the SPG7 gene and five patients (5/30, 16.7%) who harbored variants of uncertain significance close to probable pathogenicity in the genes WFS1, LOXL1, MMP19, NR2F1 and PMPCA. No pathogenic mitochondrial DNA variants were found in this group. CONCLUSIONS OCT can detect presence of asymptomatic optic neuropathy in patients with chronic alcohol use disorder. Furthermore, genetic susceptibility to optic neuropathy in this setting is found in almost a quarter of affected patients. Further studies may clarify the role of preventative measures in patients who might be predisposed to avoidable visual loss and blindness.
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Affiliation(s)
- Camille Delibes
- Département d'Ophtalmologie, Centre Hospitalier Universitaire (CHU), 49000, Angers, France
| | - Marc Ferré
- Université d'Angers, Unité Mixte de Recherche (UMR) MITOVASC, Institut National de la Santé et de la Recherche Médicale (INSERM U-1083), Centre National de la Recherche Scientifique (CNRS 6015), 49000, Angers, France
- Département de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, 49000, Angers, France
| | - Marine Rozet
- Département de Psychiatrie et d'Addictologie, Centre Hospitalier Universitaire, 49000, Angers, France
| | - Valérie Desquiret-Dumas
- Université d'Angers, Unité Mixte de Recherche (UMR) MITOVASC, Institut National de la Santé et de la Recherche Médicale (INSERM U-1083), Centre National de la Recherche Scientifique (CNRS 6015), 49000, Angers, France
- Département de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, 49000, Angers, France
| | - Alexis Descatha
- Univ. Angers (University of Angers), CHU Angers, Univ. Rennes, Inserm, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, IRSET-ESTER, SFR ICAT, CAPTV CDC, 49000, Angers, France
- Department of Occupational Medicine, Epidemiology and Prevention, Donald and Barbara Zucker School of Medicine, Hosftra University Northwell Health, New York, NY, 11021, USA
| | - Bénédicte Gohier
- Département de Psychiatrie et d'Addictologie, Centre Hospitalier Universitaire, 49000, Angers, France
- Univ Angers, Université de Nantes, LPPL, SFR CONFLUENCES, 49000, Angers, France
| | - Philippe Gohier
- Département d'Ophtalmologie, Centre Hospitalier Universitaire (CHU), 49000, Angers, France
| | - Patrizia Amati-Bonneau
- Université d'Angers, Unité Mixte de Recherche (UMR) MITOVASC, Institut National de la Santé et de la Recherche Médicale (INSERM U-1083), Centre National de la Recherche Scientifique (CNRS 6015), 49000, Angers, France
- Département de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, 49000, Angers, France
| | - Dan Milea
- Département d'Ophtalmologie, Centre Hospitalier Universitaire (CHU), 49000, Angers, France
- Singapore National Eye Centre, Singapore Eye Research Institute, Duke-NUS, Singapore, Singapore
- Rothschild Foundation Hospital, Paris, France
| | - Pascal Reynier
- Université d'Angers, Unité Mixte de Recherche (UMR) MITOVASC, Institut National de la Santé et de la Recherche Médicale (INSERM U-1083), Centre National de la Recherche Scientifique (CNRS 6015), 49000, Angers, France.
- Département de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, 49000, Angers, France.
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3
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Borna NN, Kishita Y, Shimura M, Murayama K, Ohtake A, Okazaki Y. Identification of a novel MT-ND3 variant and restoring mitochondrial function by allotopic expression of MT-ND3 gene. Mitochondrion 2024; 76:101858. [PMID: 38437941 DOI: 10.1016/j.mito.2024.101858] [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: 11/26/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Mitochondrial diseases are caused by nuclear, or mitochondrial DNA (mtDNA) variants and related co-factors. Here, we report a novel m.10197G > C variant in MT-ND3 in a patient, and two other patients with m.10191 T > C. MT-ND3 variants are known to cause Leigh syndrome or mitochondrial complex I deficiency. We performed the functional analyses of the novel m.10197G > C variant that significantly lowered MT-ND3 protein levels, causing complex I assembly and activity deficiency, and reduction of ATP synthesis. We adapted a previously described re-engineering technique of delivering mitochondrial genes into mitochondria through codon optimization for nuclear expression and translation by cytoplasmic ribosomes to rescue defects arising from the MT-ND3 variants. We constructed mitochondrial targeting sequences along with the codon-optimized MT-ND3 and imported them into the mitochondria. To achieve the goal, we imported codon-optimized MT-ND3 into mitochondria in three patients with m.10197G > C and m.10191 T > C missense variants in the MT-ND3. Nuclear expression of the MT-ND3 gene partially restored protein levels, complex I deficiency, and significant improvement of ATP production indicating a functional rescue of the mutant phenotype. The codon-optimized nuclear expression of mitochondrial protein and import inside the mitochondria can supplement the requirements for ATP in energy-deficient mitochondrial disease patients.
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Affiliation(s)
- Nurun Nahar Borna
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan; Laboratory of Genome Sciences, Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka 577-8502, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Kei Murayama
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan; Department of Pediatrics, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Moroyama, Saitama 350-0495, Japan; Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Saitama 350-0495, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan; Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
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4
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Smith KK, Moreira JD, Wilson CR, Padera JO, Lamason AN, Xue L, Gopal DM, Flynn DB, Fetterman JL. A systematic review on the biochemical threshold of mitochondrial genetic variants. Genome Res 2024; 34:341-365. [PMID: 38627095 PMCID: PMC11067886 DOI: 10.1101/gr.278200.123] [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] [Received: 06/19/2023] [Accepted: 03/15/2024] [Indexed: 05/05/2024]
Abstract
Mitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect occurs, termed the biochemical threshold. Whether the often-cited biochemical threshold of >60% VAF is similar across mtDNA variants and cell types is unclear. In our systematic review, we sought to identify the biochemical threshold of mtDNA variants in relation to VAF by human tissue/cell type. We used controlled vocabulary terms to identify articles measuring oxidative phosphorylation (OXPHOS) complex activities in relation to VAF. We identified 76 eligible publications, describing 69, 12, 16, and 49 cases for complexes I, III, IV, and V, respectively. Few studies evaluated OXPHOS activities in diverse tissue types, likely reflective of clinical access. A number of cases with similar VAFs for the same pathogenic variant had varying degrees of residual activity of the affected complex, alluding to the presence of modifying variants. Tissues and cells with VAFs <60% associated with low complex activities were described, suggesting the possibility of a biochemical threshold of <60%. Using Kendall rank correlation tests, the VAF of the m.8993T > G variant correlated with complex V activity in skeletal muscle (τ = -0.58, P = 0.01, n = 13); however, no correlation was observed in fibroblasts (P = 0.7, n = 9). Our systematic review highlights the need to investigate the biochemical threshold over a wider range of VAFs in disease-relevant cell types to better define the biochemical threshold for specific mtDNA variants.
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Affiliation(s)
- Karan K Smith
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Jesse D Moreira
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
- Programs in Human Physiology, Department of Health Sciences, Boston University Sargent College, Boston, Massachusetts 02215, USA
| | - Callum R Wilson
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - June O Padera
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Ashlee N Lamason
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Liying Xue
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Deepa M Gopal
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - David B Flynn
- Medical Sciences and Education, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Jessica L Fetterman
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA;
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5
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Fehlings DL, Zarrei M, Engchuan W, Sondheimer N, Thiruvahindrapuram B, MacDonald JR, Higginbotham EJ, Thapa R, Behlim T, Aimola S, Switzer L, Ng P, Wei J, Danthi PS, Pellecchia G, Lamoureux S, Ho K, Pereira SL, de Rijke J, Sung WWL, Mowjoodi A, Howe JL, Nalpathamkalam T, Manshaei R, Ghaffari S, Whitney J, Patel RV, Hamdan O, Shaath R, Trost B, Knights S, Samdup D, McCormick A, Hunt C, Kirton A, Kawamura A, Mesterman R, Gorter JW, Dlamini N, Merico D, Hilali M, Hirschfeld K, Grover K, Bautista NX, Han K, Marshall CR, Yuen RKC, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Maxwell G, Shevell M, Costain G, Michaud JL, Hamdan FF, Gauthier J, Uguen K, Stavropoulos DJ, Wintle RF, Oskoui M, Scherer SW. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy. Nat Genet 2024; 56:585-594. [PMID: 38553553 DOI: 10.1038/s41588-024-01686-x] [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] [Received: 12/23/2022] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
We performed whole-genome sequencing (WGS) in 327 children with cerebral palsy (CP) and their biological parents. We classified 37 of 327 (11.3%) children as having pathogenic/likely pathogenic (P/LP) variants and 58 of 327 (17.7%) as having variants of uncertain significance. Multiple classes of P/LP variants included single-nucleotide variants (SNVs)/indels (6.7%), copy number variations (3.4%) and mitochondrial mutations (1.5%). The COL4A1 gene had the most P/LP SNVs. We also analyzed two pediatric control cohorts (n = 203 trios and n = 89 sib-pair families) to provide a baseline for de novo mutation rates and genetic burden analyses, the latter of which demonstrated associations between de novo deleterious variants and genes related to the nervous system. An enrichment analysis revealed previously undescribed plausible candidate CP genes (SMOC1, KDM5B, BCL11A and CYP51A1). A multifactorial CP risk profile and substantial presence of P/LP variants combine to support WGS in the diagnostic work-up across all CP and related phenotypes.
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Affiliation(s)
- Darcy L Fehlings
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Neal Sondheimer
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ritesh Thapa
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Tarannum Behlim
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sabrina Aimola
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Lauren Switzer
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Pamela Ng
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prakroothi S Danthi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mowjoodi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shannon Knights
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Dawa Samdup
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Anna McCormick
- Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Carolyn Hunt
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Adam Kirton
- Department of Pediatrics, Department of Clinical Neuroscience, University of Calgary, Calgary, Alberta, Canada
| | - Anne Kawamura
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ronit Mesterman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Jan Willem Gorter
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Nomazulu Dlamini
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Neurosciences and Mental Health Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Deep Genomics Inc., Toronto, Ontario, Canada
- Vevo Therapeutics Inc., San Francisco, CA, USA
| | - Murto Hilali
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Hirschfeld
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kritika Grover
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nelson X Bautista
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kara Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piush Mandhane
- Faculty of Medicine & Dentistry, Pediatrics Department, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - George Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Michael Shevell
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Gregory Costain
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacques L Michaud
- Departments of Pediatrics and Neurosciences, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Julie Gauthier
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Kevin Uguen
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maryam Oskoui
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.
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6
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Ferreira RC, Rodrigues CR, Broach JR, Briones MRS. Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. Int J Mol Sci 2024; 25:3785. [PMID: 38612593 PMCID: PMC11012180 DOI: 10.3390/ijms25073785] [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: 01/25/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
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Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - Camila R. Rodrigues
- Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - James R. Broach
- Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
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7
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Płoszaj T, Skoczylas S, Gadzalska K, Jakiel P, Juścińska E, Gorządek M, Robaszkiewicz A, Borowiec M, Zmysłowska A. Screening for Rare Mitochondrial Genome Variants Reveals a Potentially Novel Association between MT-CO1 and MT-TL2 Genes and Diabetes Phenotype. Int J Mol Sci 2024; 25:2438. [PMID: 38397113 PMCID: PMC10889583 DOI: 10.3390/ijms25042438] [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: 12/08/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Variations in several nuclear genes predisposing humans to the development of MODY diabetes have been very well characterized by modern genetic diagnostics. However, recent reports indicate that variants in the mtDNA genome may also be associated with the diabetic phenotype. As relatively little research has addressed the entire mitochondrial genome in this regard, the aim of the present study is to evaluate the genetic variations present in mtDNA among individuals susceptible to MODY diabetes. In total, 193 patients with a MODY phenotype were tested with a custom panel with mtDNA enrichment. Heteroplasmic variants were selected for further analysis via further sequencing based on long-range PCR to evaluate the potential contribution of frequent NUMTs (acronym for nuclear mitochondrial DNA) insertions. Twelve extremely rare variants with a potential damaging character were selected, three of which were likely to be the result of NUMTs from the nuclear genome. The variant m.3243A>G in MT-TL1 was responsible for 3.5% of MODY cases in our study group. In addition, a novel, rare, and possibly pathogenic leucine variant m.12278T>C was found in MT-TL2. Our findings also found the MT-CO1 gene to be over-represented in the study group, with a clear phenotype-genotype correlation observed in one family. Our data suggest that heteroplasmic variants in MT-COI and MT-TL2 genes may play a role in the pathophysiology of glucose metabolism in humans.
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Affiliation(s)
- Tomasz Płoszaj
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Sebastian Skoczylas
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Karolina Gadzalska
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Paulina Jakiel
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Ewa Juścińska
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Monika Gorządek
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland;
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
| | - Agnieszka Zmysłowska
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; (S.S.); (K.G.); (P.J.); (E.J.); (M.G.); (M.B.); (A.Z.)
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8
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Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [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: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
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Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
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9
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Xu P, Yang T, Kundnani DL, Sun M, Marsili S, Gombolay A, Jeon Y, Newnam G, Balachander S, Bazzani V, Baccarani U, Park V, Tao S, Lori A, Schinazi R, Kim B, Pursell Z, Tell G, Vascotto C, Storici F. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Res 2024; 52:1207-1225. [PMID: 38117983 PMCID: PMC10853789 DOI: 10.1093/nar/gkad1204] [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] [Received: 04/28/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.
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Affiliation(s)
- Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Veronica Bazzani
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Umberto Baccarani
- Department of Medicine, University of Udine, Udine 33100, Italy
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine 33100, Italy
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta 30329, GA, USA
- Department of Population Science, American Cancer Society, Kennesaw 30144, GA, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine 33100, Italy
| | - Carlo Vascotto
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
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10
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Mertens J, Belva F, van Montfoort APA, Regin M, Zambelli F, Seneca S, Couvreu de Deckersberg E, Bonduelle M, Tournaye H, Stouffs K, Barbé K, Smeets HJM, Van de Velde H, Sermon K, Blockeel C, Spits C. Children born after assisted reproduction more commonly carry a mitochondrial genotype associating with low birthweight. Nat Commun 2024; 15:1232. [PMID: 38336715 PMCID: PMC10858059 DOI: 10.1038/s41467-024-45446-1] [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: 12/10/2022] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Children conceived through assisted reproductive technologies (ART) have an elevated risk of lower birthweight, yet the underlying cause remains unclear. Our study explores mitochondrial DNA (mtDNA) variants as contributors to birthweight differences by impacting mitochondrial function during prenatal development. We deep-sequenced the mtDNA of 451 ART and spontaneously conceived (SC) individuals, 157 mother-child pairs and 113 individual oocytes from either natural menstrual cycles or after ovarian stimulation (OS) and find that ART individuals carried a different mtDNA genotype than SC individuals, with more de novo non-synonymous variants. These variants, along with rRNA variants, correlate with lower birthweight percentiles, independent of conception mode. Their higher occurrence in ART individuals stems from de novo mutagenesis associated with maternal aging and OS-induced oocyte cohort size. Future research will establish the long-term health consequences of these changes and how these findings will impact the clinical practice and patient counselling in the future.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Aafke P A van Montfoort
- Department of Obstetrics & Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Sara Seneca
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katrien Stouffs
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Kurt Barbé
- Interfaculty Center Data Processing & Statistics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hubert J M Smeets
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- MHeNs School Institute for Mental Health and Neuroscience, GROW Institute for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hilde Van de Velde
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Department of Obstetrics and Gynaecology, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10000, Croatia
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium.
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11
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Navarro-Romero MT, Muñoz MDL, Krause-Kyora B, Cervini-Silva J, Alcalá-Castañeda E, David RE. Bioanthropological analysis of human remains from the archaic and classic period discovered in Puyil cave, Mexico. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e24903. [PMID: 38308451 DOI: 10.1002/ajpa.24903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/19/2023] [Accepted: 01/13/2024] [Indexed: 02/04/2024]
Abstract
OBJECTIVES Determine the geographic place of origin and maternal lineage of prehistoric human skeletal remains discovered in Puyil Cave, Tabasco State, Mexico, located in a region currently populated by Olmec, Zoque and Maya populations. MATERIALS AND METHODS All specimens were radiocarbon (14 C) dated (beta analytic), had dental modifications classified, and had an analysis of 13 homologous reference points conducted to evaluate artificial cranial deformation (ACD). Following DNA purification, hypervariable region I (HVR-1) of the mitogenome was amplified and Sanger sequenced. Finally, Next Generation Sequencing (NGS) was performed for total DNA. Mitochondrial DNA (mtDNA) variants and haplogroups were determined using BioEdit 7.2 and IGV software and confirmed with MITOMASTER and WebHome softwares. RESULTS Radiocarbon dating (14 C) demonstrated that the inhabitants of Puyil Cave lived during the Archaic and Classic Periods and displayed tabular oblique and tabular mimetic ACD. These pre-Hispanic remains exhibited five mtDNA lineages: A, A2, C1, C1c and D4. Network analysis revealed a close genetic affinity between pre-Hispanic Puyil Cave inhabitants and contemporary Maya subpopulations from Mexico and Guatemala, as well as individuals from Bolivia, Brazil, the Dominican Republic, and China. CONCLUSIONS Our results elucidate the dispersal of pre-Hispanic Olmec and Maya ancestors and suggest that ACD practices are closely related to Olmec and Maya practices. Additionally, we conclude that ACD has likely been practiced in the region since the Middle-Archaic Period.
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Affiliation(s)
- María Teresa Navarro-Romero
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Javiera Cervini-Silva
- Department of Process and Technology, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Enrique Alcalá-Castañeda
- Department of Archaeological Studies, Instituto Nacional de Antropología e Historia, Mexico City, Mexico
| | - Randy E David
- Department of Population Health and Disease Prevention, University of California, Irvine, Irvine, California, USA
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12
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Rogov AG, Goleva TN, Aliverdieva DA, Zvyagilskaya RA. SkQ3 Exhibits the Most Pronounced Antioxidant Effect on Isolated Rat Liver Mitochondria and Yeast Cells. Int J Mol Sci 2024; 25:1107. [PMID: 38256179 PMCID: PMC10816539 DOI: 10.3390/ijms25021107] [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: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Oxidative stress is involved in a wide range of age-related diseases. A critical role has been proposed for mitochondrial oxidative stress in initiating or promoting these pathologies and the potential for mitochondria-targeted antioxidants to fight them, making their search and testing a very urgent task. In this study, the mitochondria-targeted antioxidants SkQ1, SkQ3 and MitoQ were examined as they affected isolated rat liver mitochondria and yeast cells, comparing SkQ3 with clinically tested SkQ1 and MitoQ. At low concentrations, all three substances stimulated the oxidation of respiratory substrates in state 4 respiration (no ADP addition); at higher concentrations, they inhibited the ADP-triggered state 3 respiration and the uncoupled state, depolarized the inner mitochondrial membrane, contributed to the opening of the mPTP (mitochondrial permeability transition pore), did not specifically affect ATP synthase, and had a pronounced antioxidant effect. SkQ3 was the most active antioxidant, not possessing, unlike SkQ1 or MitoQ, prooxidant activity with increasing concentrations. In yeast cells, all three substances reduced prooxidant-induced intracellular oxidative stress and cell death and prevented and reversed mitochondrial fragmentation, with SkQ3 being the most efficient. These data allow us to consider SkQ3 as a promising potential therapeutic agent to mitigate pathologies associated with oxidative stress.
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Affiliation(s)
- Anton G. Rogov
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (A.G.R.); (T.N.G.)
| | - Tatyana N. Goleva
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (A.G.R.); (T.N.G.)
| | - Dinara A. Aliverdieva
- Precaspian Institute of Biological Resources, Daghestan Federal Research Center of the Russian Academy of Sciences, 367000 Makhachkala, Russia;
| | - Renata A. Zvyagilskaya
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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13
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Wang Z, Zhao G, Zhu Z, Wang Y, Xiang X, Zhang S, Luo T, Zhou Q, Qiu J, Tang B, Xia K, Li B, Li J. VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome. Nucleic Acids Res 2024; 52:D1478-D1489. [PMID: 37956311 PMCID: PMC10767961 DOI: 10.1093/nar/gkad1061] [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] [Received: 09/15/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
VarCards, an online database, combines comprehensive variant- and gene-level annotation data to streamline genetic counselling for coding variants. Recognising the increasing clinical relevance of non-coding variations, there has been an accelerated development of bioinformatics tools dedicated to interpreting non-coding variations, including single-nucleotide variants and copy number variations. Regrettably, most tools remain as either locally installed databases or command-line tools dispersed across diverse online platforms. Such a landscape poses inconveniences and challenges for genetic counsellors seeking to utilise these resources without advanced bioinformatics expertise. Consequently, we developed VarCards2, which incorporates nearly nine billion artificially generated single-nucleotide variants (including those from mitochondrial DNA) and compiles vital annotation information for genetic counselling based on ACMG-AMP variant-interpretation guidelines. These annotations include (I) functional effects; (II) minor allele frequencies; (III) comprehensive function and pathogenicity predictions covering all potential variants, such as non-synonymous substitutions, non-canonical splicing variants, and non-coding variations and (IV) gene-level information. Furthermore, VarCards2 incorporates 368 820 266 documented short insertions and deletions and 2 773 555 documented copy number variations, complemented by their corresponding annotation and prediction tools. In conclusion, VarCards2, by integrating over 150 variant- and gene-level annotation sources, significantly enhances the efficiency of genetic counselling and can be freely accessed at http://www.genemed.tech/varcards2/.
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Affiliation(s)
- Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhaopo Zhu
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Yijing Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xudong Xiang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shiyu Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jian Qiu
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, & Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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14
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Zhao Y, Hou Y, Zhao X, Liufu T, Yu M, Zhang W, Xie Z, Zhang VW, Yuan Y, Wang Z. The clinical, myopathological, and genetic analysis of 155 Chinese mitochondrial ophthalmoplegia patients with mitochondrial DNA single large deletions. Mol Genet Genomic Med 2024; 12:e2328. [PMID: 38018320 PMCID: PMC10767604 DOI: 10.1002/mgg3.2328] [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: 05/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Progressive external ophthalmoplegia (PEO) is a common subtype of mitochondrial encephalomyopathy. OBJECTIVE The study aimed to investigate the relationship between mitochondrial DNA (mtDNA) abnormalities, muscle pathology, and clinical manifestations in Chinese patients with single large-scale mtDNA deletion presenting with PEO. METHODS This is a retrospective single-center study. Patients with PEO who had a single large deletion in mitochondrial DNA were included in this study. The associations were analyzed between mtDNA deletion patterns, myopathological changes, and clinical characteristics. RESULTS In total, 155 patients with mitochondrial PEO carrying single large-scale mtDNA mutations were enrolled, including 137 chronic progressive external ophthalmoplegia (CPEO) and 18 Kearns-Sayre syndrome (KSS) patients. The onset ages were 9.61 ± 4.12 in KSS and 20.15 ± 9.06 in CPEO. The mtDNA deletions ranged from 2225 bp to 9131 bp, with m.8470_13446del being the most common. The KSS group showed longer deletions than the CPEO group (p = 0.004). Additionally, a higher number of deleted genes encoding respiratory chain complex subunits (p = 0.001) and tRNA genes (p = 0.009) were also observed in the KSS group. A weak negative correlation between the mtDNA deletion size and ages of onset (p < 0.001, r = -0.369) was observed. The proportion of ragged red fibers, ragged blue fibers, and cytochrome c negative fibers did not correlate significantly with onset ages (p > 0.05). However, a higher percentage of abnormal muscle fibers corresponds to an increased prevalence of exercise intolerance, limb muscle weakness, dysphagia, and cerebellar ataxia. CONCLUSION We reported a large Chinese cohort consisting of mitochondrial PEO patients with single large-scale mtDNA deletions. Our results demonstrated that the length and locations of mtDNA deletions may influence onset ages and clinical phenotypes. The severity of muscle pathology could not only indicate diagnosis but also may be associated with clinical manifestations beyond the extraocular muscles.
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Affiliation(s)
- Yang Zhao
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | - Yue Hou
- Department of GeriatricsPeking University First HospitalBeijingChina
| | - Xutong Zhao
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
- Department of NeurologyBeijing Jishuitan HospitalBeijingChina
| | - Tongling Liufu
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | - Meng Yu
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | - Wei Zhang
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | - Zhiying Xie
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | | | - Yun Yuan
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
| | - Zhaoxia Wang
- Department of NeurologyPeking University First HospitalBeijingChina
- Beijing Key Laboratory of Neurovascular Disease DiscoveryBeijingChina
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15
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Maharjan S, Gamper H, Yamaki Y, Henley RY, Li NS, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou YM. Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569632. [PMID: 38106193 PMCID: PMC10723379 DOI: 10.1101/2023.12.09.569632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.
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16
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Garcia-Gaona E, García-Gregorio A, García-Jiménez C, López-Olaiz MA, Mendoza-Ramírez P, Fernandez-Guzman D, Pillado-Sánchez RA, Soto-Pacheco AD, Yareni-Zuñiga L, Sánchez-Parada MG, González-Santiago AE, Román-Pintos LM, Castañeda-Arellano R, Hernández-Ortega LD, Mercado-Sesma AR, Orozco-Luna FDJ, Villa-Angulo C, Villa-Angulo R, Baptista-Rosas RC. mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes. Curr Issues Mol Biol 2023; 45:8716-8732. [PMID: 37998725 PMCID: PMC10670651 DOI: 10.3390/cimb45110548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Type 2 diabetes (T2D) is a chronic systemic disease with a complex etiology, characterized by insulin resistance and mitochondrial dysfunction in various cell tissues. To explore this relationship, we conducted a secondary analysis of complete mtDNA sequences from 1261 T2D patients and 1105 control individuals. Our findings revealed significant associations between certain single-nucleotide polymorphisms (SNPs) and T2D. Notably, the variants m.1438A>G (rs2001030) (controls: 32 [27.6%], T2D: 84 [72.4%]; OR: 2.46; 95%CI: 1.64-3.78; p < 0.001), m.14766C>T (rs193302980) (controls: 498 [36.9%], T2D: 853 [63.1%]; OR: 2.57, 95%CI: 2.18-3.04, p < 0.001), and m.16519T>C (rs3937033) (controls: 363 [43.4%], T2D: 474 [56.6%]; OR: 1.24, 95%CI: 1.05-1.47, p = 0.012) were significantly associated with the likelihood of developing diabetes. The variant m.16189T>C (rs28693675), which has been previously documented in several studies across diverse populations, showed no association with T2D in our analysis (controls: 148 [13.39] T2D: 171 [13.56%]; OR: 1.03; 95%CI: 0.815-1.31; p = 0.83). These results provide evidence suggesting a link between specific mtDNA polymorphisms and T2D, possibly related to association rules, topological patterns, and three-dimensional conformations associated with regions where changes occur, rather than specific point mutations in the sequence.
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Affiliation(s)
- Enrique Garcia-Gaona
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | - Alhelí García-Gregorio
- Facultad de Enfermería Región Poza Rica-Tuxpan, Universidad Veracruzana, Veracruz 91700, Mexico;
| | - Camila García-Jiménez
- Facultad de Ciencias Médicas y Biológicas “Dr. Ignacio Chávez”, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58000, Mexico;
| | | | - Paola Mendoza-Ramírez
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | | | | | - Axel David Soto-Pacheco
- Facultad de Medicina Extensión Los Mochis, Universidad Autónoma de Sinaloa, Sinaloa 81223, Mexico; (R.A.P.-S.); (A.D.S.-P.)
| | - Laura Yareni-Zuñiga
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
| | - María Guadalupe Sánchez-Parada
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Ana Elizabeth González-Santiago
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Miguel Román-Pintos
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Rolando Castañeda-Arellano
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Daniel Hernández-Ortega
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Arieh Roldán Mercado-Sesma
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | | | - Carlos Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Rafael Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Raúl C. Baptista-Rosas
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
- Hospital General de Occidente, Secretaría de Salud Jalisco, Zapopan 45170, Mexico
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17
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Hong YS, Battle SL, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake NJ, Lek M, Rotter JI, Rich SS, Kooperberg C, Reiner AP, Auer PL, Heard-Costa N, Liu C, Lai M, Murabito JM, Levy D, Grove ML, Alonso A, Gibbs R, Dugan-Perez S, Gondek LP, Guallar E, Arking DE. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nat Commun 2023; 14:6113. [PMID: 37777527 PMCID: PMC10542802 DOI: 10.1038/s41467-023-41785-7] [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: 05/14/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Mitochondria carry their own circular genome and disruption of the mitochondrial genome is associated with various aging-related diseases. Unlike the nuclear genome, mitochondrial DNA (mtDNA) can be present at 1000 s to 10,000 s copies in somatic cells and variants may exist in a state of heteroplasmy, where only a fraction of the DNA molecules harbors a particular variant. We quantify mtDNA heteroplasmy in 194,871 participants in the UK Biobank and find that heteroplasmy is associated with a 1.5-fold increased risk of all-cause mortality. Additionally, we functionally characterize mtDNA single nucleotide variants (SNVs) using a constraint-based score, mitochondrial local constraint score sum (MSS) and find it associated with all-cause mortality, and with the prevalence and incidence of cancer and cancer-related mortality, particularly leukemia. These results indicate that mitochondria may have a functional role in certain cancers, and mitochondrial heteroplasmic SNVs may serve as a prognostic marker for cancer, especially for leukemia.
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Affiliation(s)
- Yun Soo Hong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie L Battle
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Natural Sciences, College of Arts and Sciences, Bowie State University, Bowie, MD, USA
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vamsee Pillalamarri
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaqi Xie
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nancy Heard-Costa
- Departments of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Meng Lai
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Joanne M Murabito
- Section of General Internal Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Megan L Grove
- Human Genetics Center; Department of Epidemiology, Human Genetics, and Environmental Sciences; School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Eliseo Guallar
- Department of Epidemiology and Medicine, and Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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18
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [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: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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19
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Mauring L, Puusepp S, Parik M, Roomets E, Teek R, Reimand T, Pajusalu S, Kaljurand K, Õunap K. Autosomal recessive Leber's hereditary optic neuropathy caused by a homozygous variant in DNAJC30 gene. Eur J Med Genet 2023; 66:104821. [PMID: 37579815 DOI: 10.1016/j.ejmg.2023.104821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/18/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Recently, Stenton et al. (2021) described a new, autosomal recessive inheritance pattern of Leber's hereditary optic neuropathy (LHON) caused by missense variants in the DNAJC30 gene. The DNAJC30 c.152A > G, p.(Tyr51Cys) variant was by far the most common variant reported in patients originating from Eastern Europe, therefore, it is believed to be a founder variant in these populations. We report the first two cases of DNAJC30-linked autosomal recessive LHON in a young male and a female originating from Estonia. The patients presented severe loss of central vision and clinical features indistinguishable from mitochondrial LHON. The whole exome sequencing carried out in the male patient and the next-generation sequencing panel in the young female patient identified the same homozygous missense variant in the DNAJC30 gene. Our cases further reinforce the pathogenicity of c.152A > G, p.(Tyr51Cys) DNAJC30 variant causing autosomal recessive LHON. According to the gnomAD database, the allele frequency of this variant in the Estonian population is 0.8%, translating into a prevalence of carriers of 1:60. It is the highest among different gnomAD populations. Applying the Hardy-Weinberg equation, an estimated 92 persons in the Estonian population carry the homozygous variant c.152A > G, p.(Tyr51Cys) in DNAJC30. In patients with LHON, we advise sequencing both the DNAJC30 gene and mitochondrial DNA simultaneously.
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Affiliation(s)
- L Mauring
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia; Eye Clinic, Tartu University Hospital, Tartu, Estonia.
| | - S Puusepp
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - M Parik
- Eye Clinic, Tartu University Hospital, Tartu, Estonia
| | - E Roomets
- Tallinn's Children's Hospital, Tallinn, Estonia
| | - R Teek
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - T Reimand
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - S Pajusalu
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - K Kaljurand
- Eye Clinic, Tartu University Hospital, Tartu, Estonia; Department of Eye Clinic, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - K Õunap
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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20
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Shen-Gunther J, Gunther RS, Cai H, Wang Y. A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping. Int J Mol Sci 2023; 24:13505. [PMID: 37686313 PMCID: PMC10488239 DOI: 10.3390/ijms241713505] [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: 07/25/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA
| | - Rutger S. Gunther
- Nuclear Medicine & Molecular Imaging, Department of Radiology, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;
| | - Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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21
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Piotrowska-Nowak A, Safranow K, Adamczyk JG, Sołtyszewski I, Cięszczyk P, Tońska K, Żekanowski C, Borzemska B. Mitochondrial Genome Variation in Polish Elite Athletes. Int J Mol Sci 2023; 24:12992. [PMID: 37629173 PMCID: PMC10454803 DOI: 10.3390/ijms241612992] [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: 07/26/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Energy efficiency is one of the fundamental athletic performance-affecting features of the cell and the organism as a whole. Mitochondrial DNA (mtDNA) variants and haplogroups have been linked to the successful practice of various sports, but despite numerous studies, understanding of the correlation is far from being comprehensive. In this study, the mtDNA sequence and copy number were determined for 99 outstanding Polish male athletes performing in power (n = 52) or endurance sports (n = 47) and 100 controls. The distribution of haplogroups, single nucleotide variant association, heteroplasmy, and mtDNA copy number were analyzed in the blood and saliva. We found no correlation between any haplogroup, single nucleotide variant, especially rare or non-synonymous ones, and athletic performance. Interestingly, heteroplasmy was less frequent in the study group, especially in endurance athletes. We observed a lower mtDNA copy number in both power and endurance athletes compared to controls. This could result from an inactivity of compensatory mechanisms activated by disadvantageous variants present in the general population and indicates a favorable genetic makeup of the athletes. The results emphasize a need for a more comprehensive analysis of the involvement of the mitochondrial genome in physical performance, combining nucleotide and copy number analysis in the context of nuclear gene variants.
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Affiliation(s)
- Agnieszka Piotrowska-Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 5a Pawińskiego Street, 02-106 Warszawa, Poland; (A.P.-N.); (K.T.)
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland;
| | - Jakub G. Adamczyk
- Department of Theory of Sport, Józef Piłsudski University of Physical Education, Marymoncka 34 Street, 00-968 Warszawa, Poland;
| | - Ireneusz Sołtyszewski
- Department of Forensic Medicine, Medical University of Warsaw, Oczki 1 Street, 02-007 Warszawa, Poland;
| | - Paweł Cięszczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Górskiego 1 Street, 80-336 Gdansk, Poland; (P.C.); (C.Ż.)
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 5a Pawińskiego Street, 02-106 Warszawa, Poland; (A.P.-N.); (K.T.)
| | - Cezary Żekanowski
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Górskiego 1 Street, 80-336 Gdansk, Poland; (P.C.); (C.Ż.)
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5 Street, 02-106 Warszawa, Poland
| | - Beata Borzemska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Górskiego 1 Street, 80-336 Gdansk, Poland; (P.C.); (C.Ż.)
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22
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Bianco SD, Parca L, Petrizzelli F, Biagini T, Giovannetti A, Liorni N, Napoli A, Carella M, Procaccio V, Lott MT, Zhang S, Vescovi AL, Wallace DC, Caputo V, Mazza T. APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants. Nat Commun 2023; 14:5058. [PMID: 37598215 PMCID: PMC10439926 DOI: 10.1038/s41467-023-40797-7] [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: 01/23/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Mitochondrial dysfunction has pleiotropic effects and is frequently caused by mitochondrial DNA mutations. However, factors such as significant variability in clinical manifestations make interpreting the pathogenicity of variants in the mitochondrial genome challenging. Here, we present APOGEE 2, a mitochondrially-centered ensemble method designed to improve the accuracy of pathogenicity predictions for interpreting missense mitochondrial variants. Built on the joint consensus recommendations by the American College of Medical Genetics and Genomics/Association for Molecular Pathology, APOGEE 2 features an improved machine learning method and a curated training set for enhanced performance metrics. It offers region-wise assessments of genome fragility and mechanistic analyses of specific amino acids that cause perceptible long-range effects on protein structure. With clinical and research use in mind, APOGEE 2 scores and pathogenicity probabilities are precompiled and available in MitImpact. APOGEE 2's ability to address challenges in interpreting mitochondrial missense variants makes it an essential tool in the field of mitochondrial genetics.
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Affiliation(s)
- Salvatore Daniele Bianco
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Parca
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Italian Space Agency, Rome, Italy
| | - Francesco Petrizzelli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Tommaso Biagini
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Agnese Giovannetti
- Clinical Genomics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Niccolò Liorni
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Napoli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, (FG), Italy
| | - Vincent Procaccio
- University of Angers, Genetics Department CHU Angers, Mitolab UMR CNRS 6015-INSERM U1083, F-49000, Angers, France
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angelo Luigi Vescovi
- ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCSS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Mazza
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy.
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23
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Tomoda E, Nagao A, Shirai Y, Asano K, Suzuki T, Battersby B, Suzuki T. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases. Nucleic Acids Res 2023; 51:7563-7579. [PMID: 36928678 PMCID: PMC10415153 DOI: 10.1093/nar/gkad139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/14/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Mutations in mitochondrial (mt-)tRNAs frequently cause mitochondrial dysfunction. Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and myoclonus epilepsy associated with ragged red fibers (MERRF) are major clinical subgroups of mitochondrial diseases caused by pathogenic point mutations in tRNA genes encoded in mtDNA. We previously reported a severe reduction in the frequency of 5-taurinomethyluridine (τm5U) and its 2-thiouridine derivative (τm5s2U) in the anticodons of mutant mt-tRNAs isolated from the cells of patients with MELAS and MERRF, respectively. The hypomodified tRNAs fail to decode cognate codons efficiently, resulting in defective translation of respiratory chain proteins in mitochondria. To restore the mitochondrial activity of MELAS patient cells, we overexpressed MTO1, a τm5U-modifying enzyme, in patient-derived myoblasts. We used a newly developed primer extension method and showed that MTO1 overexpression almost completely restored the τm5U modification of the MELAS mutant mt-tRNALeu(UUR). An increase in mitochondrial protein synthesis and oxygen consumption rate suggested that the mitochondrial function of MELAS patient cells can be activated by restoring the τm5U of the mutant tRNA. In addition, we confirmed that MTO1 expression restored the τm5s2U of the mutant mt-tRNALys in MERRF patient cells. These findings pave the way for epitranscriptomic therapies for mitochondrial diseases.
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Affiliation(s)
- Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Shirai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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24
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Ijuin A, Ueno H, Hayama T, Miyai S, Miyakoshi A, Hamada H, Sueyoshi S, Tochihara S, Saito M, Hamanoue H, Takeshima T, Yumura Y, Miyagi E, Kurahashi H, Sakakibara H, Murase M. Mitochondrial DNA mutations can influence the post-implantation development of human mosaic embryos. Front Cell Dev Biol 2023; 11:1215626. [PMID: 37635871 PMCID: PMC10451077 DOI: 10.3389/fcell.2023.1215626] [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: 05/02/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction: Several healthy euploid births have been reported following the transfer of mosaic embryos, including both euploid and aneuploid blastomeres. This has been attributed to a reduced number of aneuploid cells, as previously reported in mice, but remains poorly explored in humans. We hypothesized that mitochondrial function, one of the most critical factors for embryonic development, can influence human post-implantation embryonic development, including a decrease of aneuploid cells in mosaic embryos. Methods: To clarify the role of mitochondrial function, we biopsied multiple parts of each human embryo and observed the remaining embryos under in vitro culture as a model of post-implantation development (n = 27 embryos). Karyotyping, whole mitochondrial DNA (mtDNA) sequencing, and mtDNA copy number assays were performed on all pre- and post-culture samples. Results: The ratio of euploid embryos was significantly enhanced during in vitro culture, whereas the ratio of mosaic embryos was significantly reduced. Furthermore, post-culture euploid and culturable embryos had significantly few mtDNA mutations, although mtDNA copy numbers did not differ. Discussion: Our results indicate that aneuploid cells decrease in human embryos post-implantation, and mtDNA mutations might induce low mitochondrial function and influence the development of post-implantation embryos with not only aneuploidy but also euploidy. Analyzing the whole mtDNA mutation number may be a novel method for selecting a better mosaic embryo for transfer.
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Affiliation(s)
- Akifumi Ijuin
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
- Department of OB and GYN, Yokohama City University School of Medicine Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Hiroe Ueno
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Tomonari Hayama
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
- Department of GYN, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Shunsuke Miyai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Ai Miyakoshi
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Haru Hamada
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Sumiko Sueyoshi
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
- Department of OB and GYN, Yokohama City University School of Medicine Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Shiori Tochihara
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Marina Saito
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Haruka Hamanoue
- Department of Clinical Genetics, Faculty of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Teppei Takeshima
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Yasushi Yumura
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Etsuko Miyagi
- Department of OB and GYN, Yokohama City University School of Medicine Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Hideya Sakakibara
- Department of GYN, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
| | - Mariko Murase
- Reproduction Center, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan
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25
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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26
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Mullin NK, Voigt AP, Flamme-Wiese MJ, Liu X, Riker MJ, Varzavand K, Stone EM, Tucker BA, Mullins RF. Multimodal single-cell analysis of nonrandom heteroplasmy distribution in human retinal mitochondrial disease. JCI Insight 2023; 8:e165937. [PMID: 37289546 PMCID: PMC10443808 DOI: 10.1172/jci.insight.165937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
Variants within the high copy number mitochondrial genome (mtDNA) can disrupt organelle function and lead to severe multisystem disease. The wide range of manifestations observed in patients with mitochondrial disease results from varying fractions of abnormal mtDNA molecules in different cells and tissues, a phenomenon termed heteroplasmy. However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. Here, we identify nonrandom distribution of a pathogenic mtDNA variant across a complex tissue using single-cell RNA-Seq, mitochondrial single-cell ATAC sequencing, and multimodal single-cell sequencing. We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. Utilizing the retina as a model for complex multilineage tissues, we found that the proportion of the pathogenic m.3243A>G allele was neither evenly nor randomly distributed across diverse cell types. All neuroectoderm-derived neural cells exhibited a high percentage of the mutant variant. However, a subset of mesoderm-derived lineage, namely the vasculature of the choroid, was near homoplasmic for the WT allele. Gene expression and chromatin accessibility profiles of cell types with high and low proportions of m.3243A>G implicate mTOR signaling in the cellular response to heteroplasmy. We further found by multimodal single-cell sequencing of retinal pigment epithelial cells that a high proportion of the pathogenic mtDNA variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings show the nonrandom nature of mitochondrial variant partitioning in human mitochondrial disease and underscore its implications for mitochondrial disease pathogenesis and treatment.
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Affiliation(s)
- Nathaniel K. Mullin
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Andrew P. Voigt
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Miles J. Flamme-Wiese
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Xiuying Liu
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Megan J. Riker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Katayoun Varzavand
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Edwin M. Stone
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Budd A. Tucker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Robert F. Mullins
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
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27
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Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet 2023; 55:1198-1209. [PMID: 37386249 PMCID: PMC10548551 DOI: 10.1038/s41588-023-01433-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.
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Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yu-Hsin Hsieh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Kopal Garg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pauline Kautz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Technische Universität Berlin, Institute of Biotechnology, Berlin, Germany
| | - Lena Nitsch
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Samantha D Praktiknjo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Maschmeyer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jeffrey M Verboon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- Immunai, New York City, NY, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rhea Malhotra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumit Parikh
- Center for Pediatric Neurosciences, Mitochondrial Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lena Oevermann
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Johannes Schulte
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- 10x Genomics, San Francisco, CA, USA
| | | | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
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28
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Smullen M, Olson MN, Murray LF, Suresh M, Yan G, Dawes P, Barton NJ, Mason JN, Zhang Y, Fernandez-Fontaine AA, Church GM, Mastroeni D, Wang Q, Lim ET, Chan Y, Readhead B. Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G. Sci Rep 2023; 13:10405. [PMID: 37369829 DOI: 10.1038/s41598-023-37541-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimer's disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT heteroplasmy was present throughout the entire MT genome for blood samples, we detected MT heteroplasmy only within the MT control region for brain samples. We observed that an MT variant 10398A>G (rs2853826) was significantly associated with overall MT heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci.
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Affiliation(s)
- Molly Smullen
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Meagan N Olson
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Liam F Murray
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Madhusoodhanan Suresh
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Guang Yan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Pepper Dawes
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nathaniel J Barton
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jivanna N Mason
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Yucheng Zhang
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Aria A Fernandez-Fontaine
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Elaine T Lim
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Yingleong Chan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
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Gedikbasi A, Toksoy G, Karaca M, Gulec C, Balci MC, Gunes D, Gunes S, Aslanger AD, Unverengil G, Karaman B, Basaran S, Demirkol M, Gokcay GF, Uyguner ZO. Clinical and bi-genomic DNA findings of patients suspected to have mitochondrial diseases. Front Genet 2023; 14:1191159. [PMID: 37377599 PMCID: PMC10292751 DOI: 10.3389/fgene.2023.1191159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/02/2023] [Indexed: 06/29/2023] Open
Abstract
Background: Mitochondrial diseases are the most common group of inherited metabolic disorders, causing difficulties in definite diagnosis due to clinical and genetic heterogeneity. Clinical components are predominantly associated with pathogenic variants shown in nuclear or mitochondrial genomes that affect vital respiratory chain function. The development of high-throughput sequencing technologies has accelerated the elucidation of the genetic etiology of many genetic diseases that previously remained undiagnosed. Methods: Thirty affected patients from 24 unrelated families with clinical, radiological, biochemical, and histopathological evaluations considered for mitochondrial diseases were investigated. DNA isolated from the peripheral blood samples of probands was sequenced for nuclear exome and mitochondrial DNA (mtDNA) analyses. MtDNA sequencing was also performed from the muscle biopsy material in one patient. For segregation, Sanger sequencing is performed for pathogenic alterations in five other affected family members and healthy parents. Results: Exome sequencing revealed 14 different pathogenic variants in nine genes encoding mitochondrial function peptides (AARS2, EARS2, ECHS1, FBXL4, MICOS13, NDUFAF6, OXCT1, POLG, and TK2) in 12 patients from nine families and four variants in genes encoding important for muscle structure (CAPN3, DYSF, and TCAP) in six patients from four families. Three probands carried pathogenic mtDNA variations in two genes (MT-ATP6 and MT-TL1). Nine variants in five genes are reported for the first time with disease association: (AARS2: c.277C>T/p.(R93*), c.845C>G/p.(S282C); EARS2: c.319C>T/p.(R107C), c.1283delC/p.(P428Lfs*); ECHS1: c.161G>A/p.(R54His); c.202G>A/p.(E68Lys); NDUFAF6: c.479delA/p.(N162Ifs*27); and OXCT1: c.1370C>T/p.(T457I), c.1173-139G>T/p.(?). Conclusion: Bi-genomic DNA sequencing clarified genetic etiology in 67% (16/24) of the families. Diagnostic utility by mtDNA sequencing in 13% (3/24) and exome sequencing in 54% (13/24) of the families prioritized searching for nuclear genome pathologies for the first-tier test. Weakness and muscle wasting observed in 17% (4/24) of the families underlined that limb-girdle muscular dystrophy, similar to mitochondrial myopathy, is an essential point for differential diagnosis. The correct diagnosis is crucial for comprehensive genetic counseling of families. Also, it contributes to making treatment-helpful referrals, such as ensuring early access to medication for patients with mutations in the TK2 gene.
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Affiliation(s)
- Asuman Gedikbasi
- Department of Pediatric Basic Sciences, Institute of Child Health Istanbul University, Istanbul, Türkiye
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Guven Toksoy
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Meryem Karaca
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Cagri Gulec
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Mehmet Cihan Balci
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Dilek Gunes
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Seda Gunes
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Ayca Dilruba Aslanger
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Gokcen Unverengil
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Birsen Karaman
- Department of Pediatric Basic Sciences, Institute of Child Health Istanbul University, Istanbul, Türkiye
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Seher Basaran
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Mubeccel Demirkol
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Gulden Fatma Gokcay
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
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30
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Xing S, Jiang S, Wang S, Lin P, Sun H, Peng H, Yang J, Kong H, Wang S, Bai Q, Qiu R, Dai W, Yuan J, Ma Y, Yu X, Yao Y, Su J. Association of mitochondrial DNA variation with high myopia in a Han Chinese population. Mol Genet Genomics 2023:10.1007/s00438-023-02036-y. [PMID: 37277661 PMCID: PMC10363046 DOI: 10.1007/s00438-023-02036-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
High myopia (HM), which is characterized by oxidative stress, is one of the leading causes of visual impairment and blindness across the world. Family and population genetic studies have uncovered nuclear-genome variants in proteins functioned in the mitochondria. However, whether mitochondrial DNA mutations are involved in HM remains unexplored. Here, we performed the first large-scale whole-mitochondrial genome study in 9613 HM cases and 9606 control subjects of Han Chinese ancestry for identifying HM-associated mitochondrial variants. The single-variant association analysis identified nine novel genetic variants associated with HM reaching the entire mitochondrial wide significance level, including rs370378529 in ND2 with an odds ratio (OR) of 5.25. Interestingly, eight out of nine variants were predominantly located in related sub-haplogroups, i.e. m.5261G > A in B4b1c, m.12280A > G in G2a4, m.7912G > A in D4a3b, m.94G > A in D4e1, m.14857 T > C in D4e3, m.14280A > G in D5a2, m.16272A > G in G2a4, m.8718A > G in M71 and F1a3, indicating that the sub-haplogroup background can increase the susceptible risk for high myopia. The polygenic risk score analysis of the target and validation cohorts indicated a high accuracy for predicting HM with mtDNA variants (AUC = 0.641). Cumulatively, our findings highlight the critical roles of mitochondrial variants in untangling the genetic etiology of HM.
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Affiliation(s)
- Shilai Xing
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyi Jiang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Haojun Sun
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hui Peng
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jiaying Yang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengte Kong
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sheng Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingshi Bai
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ruowen Qiu
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Jian Yuan
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Yunlong Ma
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou, 325024, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
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31
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Vandiver AR, Hoang AN, Herbst A, Lee CC, Aiken JM, McKenzie D, Teitell MA, Timp W, Wanagat J. Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging. Aging Cell 2023; 22:e13842. [PMID: 37132288 PMCID: PMC10265159 DOI: 10.1111/acel.13842] [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: 01/09/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next-generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency. We employed nanopore Cas9-targeted sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints. NCATS-mtDNA sequencing allows the identification of mtDNA deletions on a single-molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.
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Affiliation(s)
- Amy R. Vandiver
- Division of Dermatology, Department of MedicineUCLALos AngelesCaliforniaUSA
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
| | - Austin N. Hoang
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Allen Herbst
- US Geological Survey National Wildlife Health CenterMadisonWisconsinUSA
| | - Cathy C. Lee
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Judd M. Aiken
- Department of Agricultural, Food and Nutritional SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Debbie McKenzie
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael A. Teitell
- Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pathology and Laboratory Medicine, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Bioengineering, California NanoSystems Institute, Broad Center for Regenerative Medicine and Stem Cell ResearchUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pediatrics, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer Center, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
| | - Winston Timp
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
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32
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Rákosníková T, Kelifová S, Štufková H, Lokvencová K, Lišková P, Kousal B, Honzík T, Hansíková H, Martínek V, Tesařová M. Case report: A rare variant m.4135T>C in the MT-ND1 gene leads to Leber hereditary optic neuropathy and altered respiratory chain supercomplexes. Front Genet 2023; 14:1182288. [PMID: 37274791 PMCID: PMC10233053 DOI: 10.3389/fgene.2023.1182288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
Leber hereditary optic neuropathy is a primary mitochondrial disease characterized by acute visual loss due to the degeneration of retinal ganglion cells. In this study, we describe a patient carrying a rare missense heteroplasmic variant in MT-ND1, NC_012920.1:m.4135T>C (p.Tyr277His) manifesting with a typical bilateral painless decrease of the visual function, triggered by physical exercise or higher ambient temperature. Functional studies in muscle and fibroblasts show that amino acid substitution Tyr277 with His leads to only a negligibly decreased level of respiratory chain complex I (CI), but the formation of supercomplexes and the activity of the enzyme are disturbed noticeably. Our data indicate that although CI is successfully assembled in the patient's mitochondria, its function is hampered by the m.4135T>C variant, probably by stabilizing CI in its inactive form. We conclude that the m.4135T>C variant together with a combination of external factors is necessary to manifest the phenotype.
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Affiliation(s)
- Tereza Rákosníková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Silvie Kelifová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Hana Štufková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Kateřina Lokvencová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Petra Lišková
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Bohdan Kousal
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Tomáš Honzík
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Hana Hansíková
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czechia
| | - Markéta Tesařová
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
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33
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Otsuka T, Matsui H. Fish Models for Exploring Mitochondrial Dysfunction Affecting Neurodegenerative Disorders. Int J Mol Sci 2023; 24:ijms24087079. [PMID: 37108237 PMCID: PMC10138900 DOI: 10.3390/ijms24087079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Neurodegenerative disorders are characterized by the progressive loss of neuronal structure or function, resulting in memory loss and movement disorders. Although the detailed pathogenic mechanism has not been elucidated, it is thought to be related to the loss of mitochondrial function in the process of aging. Animal models that mimic the pathology of a disease are essential for understanding human diseases. In recent years, small fish have become ideal vertebrate models for human disease due to their high genetic and histological homology to humans, ease of in vivo imaging, and ease of genetic manipulation. In this review, we first outline the impact of mitochondrial dysfunction on the progression of neurodegenerative diseases. Then, we highlight the advantages of small fish as model organisms, and present examples of previous studies regarding mitochondria-related neuronal disorders. Lastly, we discuss the applicability of the turquoise killifish, a unique model for aging research, as a model for neurodegenerative diseases. Small fish models are expected to advance our understanding of the mitochondrial function in vivo, the pathogenesis of neurodegenerative diseases, and be important tools for developing therapies to treat diseases.
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Affiliation(s)
- Takayoshi Otsuka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
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34
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Mishra Y, Kumar Kaundal R. Role of SIRT3 in mitochondrial biology and its therapeutic implications in neurodegenerative disorders. Drug Discov Today 2023; 28:103583. [PMID: 37028501 DOI: 10.1016/j.drudis.2023.103583] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023]
Abstract
Sirtuin 3 (SIRT3), a mitochondrial deacetylase expressed preferentially in high-metabolic-demand tissues including the brain, requires NAD+ as a cofactor for catalytic activity. It regulates various processes such as energy homeostasis, redox balance, mitochondrial quality control, mitochondrial unfolded protein response (UPRmt), biogenesis, dynamics and mitophagy by altering protein acetylation status. Reduced SIRT3 expression or activity causes hyperacetylation of hundreds of mitochondrial proteins, which has been linked with neurological abnormalities, neuro-excitotoxicity and neuronal cell death. A body of evidence has suggested, SIRT3 activation as a potential therapeutic modality for age-related brain abnormalities and neurodegenerative disorders.
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Affiliation(s)
- Yogesh Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow (UP)-226002, India
| | - Ravinder Kumar Kaundal
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow (UP)-226002, India.
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35
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:ijms24065798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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36
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Boughanem H, Böttcher Y, Tomé-Carneiro J, López de Las Hazas MC, Dávalos A, Cayir A, Macias-González M. The emergent role of mitochondrial RNA modifications in metabolic alterations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1753. [PMID: 35872632 DOI: 10.1002/wrna.1753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial epitranscriptomics refers to the modifications occurring in all the different RNA types of mitochondria. Although the number of mitochondrial RNA modifications is less than those in cytoplasm, substantial evidence indicates that they play a critical role in accurate protein synthesis. Recent evidence supported those modifications in mitochondrial RNAs also have crucial implications in mitochondrial-related diseases. In the light of current knowledge about the involvement, the association between mitochondrial RNA modifications and diseases arises from studies focusing on mutations in both mitochondrial and nuclear DNA genes encoding enzymes involved in such modifications. Here, we review the current evidence available for mitochondrial RNA modifications and their role in metabolic disorders, and we also explore the possibility of using them as promising targets for prevention and early detection. Finally, we discuss future directions of mitochondrial epitranscriptomics in these metabolic alterations, and how these RNA modifications may offer a new diagnostic and theragnostic avenue for preventive purposes. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
| | - João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Manuel Macias-González
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
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37
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Fontana GA, Gahlon HL. Detection of UV-Induced Deletions in Mitochondrial DNA. Methods Mol Biol 2023; 2615:281-292. [PMID: 36807799 DOI: 10.1007/978-1-0716-2922-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations are found in several human pathologies and are associated with aging. Deletion mutations in mtDNA result in the loss of essential genes for mitochondrial function. Over 250 deletion mutations have been reported and the common deletion is the most frequent mtDNA deletion linked to disease. This deletion removes 4977 base pairs of mtDNA. It has previously been shown that exposure to UVA radiation can promote the formation of the common deletion. Furthermore, aberrations in mtDNA replication and repair are associated with formation of the common deletion. However, molecular mechanisms describing the formation of this deletion are poorly characterized. This chapter describes a method to irradiate human skin fibroblasts with physiological doses of UVA and the subsequent detection of the common deletion by quantitative PCR analysis.
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Affiliation(s)
- Gabriele A Fontana
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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38
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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39
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Giannikou K, Martin KR, Abdel-Azim AG, Pamir KJ, Hougard TR, Bagwe S, Tang Y, MacKeigan JP, Kwiatkowski DJ, Henske EP, Lam HC. Spectrum of germline and somatic mitochondrial DNA variants in Tuberous Sclerosis Complex. Front Genet 2023; 13:917993. [PMID: 36793390 PMCID: PMC9923026 DOI: 10.3389/fgene.2022.917993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/23/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function variants in either TSC1 or TSC2 and is characterized by broad phenotypic heterogeneity. Currently, there is limited knowledge regarding the role of the mitochondrial genome (mtDNA) in TSC pathogenesis. In this study, we aimed to determine the prevalence and spectrum of germline and somatic mtDNA variants in TSC and identify potential disease modifiers. Analysis of mtDNA amplicon massively parallel sequencing (aMPS) data, off-target mtDNA from whole-exome sequencing (WES), and/or qPCR, revealed mtDNA alterations in 270 diverse tissues (139 TSC-associated tumors and 131 normal tissue samples) from 199 patients and six healthy individuals. Correlation of clinical features to mtDNA variants and haplogroup analysis was done in 102 buccal swabs (age: 20-71 years). No correlation was found between clinical features and either mtDNA variants or haplogroups. No pathogenic variants were identified in the buccal swab samples. Using in silico analysis, we identified three predicted pathogenic variants in tumor samples: MT-ND4 (m.11742G>A, p. Cys328Tyr, VAF: 43%, kidney angiomyolipoma), MT-CYB (m.14775T>C, p. Leu10Pro, VAF: 43%, LAM abdominal tumor) and MT-CYB (m.15555C>T, p. Pro270Leu, VAF: 7%, renal cell carcinoma). Large deletions of the mitochondrial genome were not detected. Analysis of tumors from 23 patients with corresponding normal tissue did not reveal any recurrent tumor-associated somatic variants. The mtDNA/gDNA ratio between tumors and corresponding normal tissue was also unchanged. Overall, our findings demonstrate that the mitochondrial genome is highly stable across tissues and within TSC-associated tumors.
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Affiliation(s)
- Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
- Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Katie R. Martin
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Ahmad G. Abdel-Azim
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Kaila J. Pamir
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Thomas R. Hougard
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Shefali Bagwe
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Yan Tang
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Jeffrey P. MacKeigan
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Elizabeth P. Henske
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Hilaire C. Lam
- Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
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40
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [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: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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41
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Younger DS. Neurogenetic motor disorders. HANDBOOK OF CLINICAL NEUROLOGY 2023; 195:183-250. [PMID: 37562870 DOI: 10.1016/b978-0-323-98818-6.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Advances in the field of neurogenetics have practical applications in rapid diagnosis on blood and body fluids to extract DNA, obviating the need for invasive investigations. The ability to obtain a presymptomatic diagnosis through genetic screening and biomarkers can be a guide to life-saving disease-modifying therapy or enzyme replacement therapy to compensate for the deficient disease-causing enzyme. The benefits of a comprehensive neurogenetic evaluation extend to family members in whom identification of the causal gene defect ensures carrier detection and at-risk counseling for future generations. This chapter explores the many facets of the neurogenetic evaluation in adult and pediatric motor disorders as a primer for later chapters in this volume and a roadmap for the future applications of genetics in neurology.
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Affiliation(s)
- David S Younger
- Department of Clinical Medicine and Neuroscience, CUNY School of Medicine, New York, NY, United States; Department of Medicine, Section of Internal Medicine and Neurology, White Plains Hospital, White Plains, NY, United States.
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42
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Willis JCW, Silva-Pinheiro P, Widdup L, Minczuk M, Liu DR. Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo. Nat Commun 2022; 13:7204. [PMID: 36418298 PMCID: PMC9684478 DOI: 10.1038/s41467-022-34784-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) use programmable DNA-binding TALE repeat arrays, rather than CRISPR proteins, a split double-stranded DNA cytidine deaminase (DddA), and a uracil glycosylase inhibitor to mediate C•G-to-T•A editing in nuclear and organelle DNA. Here we report the development of zinc finger DdCBEs (ZF-DdCBEs) and the improvement of their editing performance through engineering their architectures, defining improved ZF scaffolds, and installing DddA activity-enhancing mutations. We engineer variants with improved DNA specificity by integrating four strategies to reduce off-target editing. We use optimized ZF-DdCBEs to install or correct disease-associated mutations in mitochondria and in the nucleus. Leveraging their small size, we use a single AAV9 to deliver into heart, liver, and skeletal muscle in post-natal mice ZF-DdCBEs that efficiently install disease-associated mutations. While off-target editing of ZF-DdCBEs is likely too high for therapeutic applications, these findings demonstrate a compact, all-protein base editing research tool for precise editing of organelle or nuclear DNA without double-strand DNA breaks.
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Affiliation(s)
- Julian C W Willis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | | | - Lily Widdup
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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43
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Alkhaldi HA, Phan DH, Vik SB. Analysis of Human Clinical Mutations of Mitochondrial ND1 in a Bacterial Model System for Complex I. Life (Basel) 2022; 12:1934. [PMID: 36431069 PMCID: PMC9696053 DOI: 10.3390/life12111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The most common causes of mitochondrial dysfunction and disease include mutations in subunits and assembly factors of Complex I. Numerous mutations in the mitochondrial gene ND1 have been identified in humans. Currently, a bacterial model system provides the only method for rapid construction and analysis of mutations in homologs of human ND1. In this report, we have identified nine mutations in human ND1 that are reported to be pathogenic and are located at subunit interfaces. Our hypothesis was that these mutations would disrupt Complex I assembly. Seventeen mutations were constructed in the homologous nuoH gene in an E. coli model system. In addition to the clinical mutations, alanine substitutions were constructed in order to distinguish between a deleterious effect from the introduction of the mutant residue and the loss of the original residue. The mutations were moved to an expression vector containing all thirteen genes of the E. coli nuo operon coding for Complex I. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity and proton translocation were measured. Samples were also tested for assembly by native gel electrophoresis and for expression of NuoH by immunoblotting. A range of outcomes was observed: Mutations at four of the sites allow normal assembly with moderate activity (50−76% of wild type). Mutations at the other sites disrupt assembly and/or activity, and in some cases the outcomes depend upon the amino acid introduced. In general, the outcomes are consistent with the proposed pathogenicity in humans.
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Affiliation(s)
| | | | - Steven B. Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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44
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Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, Loureiro LO, Reuter MS, Roshandel D, Whitney J, Zarrei M, Bookman M, Somerville C, Shaath R, Abdi M, Aliyev E, Patel RV, Nalpathamkalam T, Pellecchia G, Hamdan O, Kaur G, Wang Z, MacDonald JR, Wei J, Sung WWL, Lamoureux S, Hoang N, Selvanayagam T, Deflaux N, Geng M, Ghaffari S, Bates J, Young EJ, Ding Q, Shum C, D'Abate L, Bradley CA, Rutherford A, Aguda V, Apresto B, Chen N, Desai S, Du X, Fong MLY, Pullenayegum S, Samler K, Wang T, Ho K, Paton T, Pereira SL, Herbrick JA, Wintle RF, Fuerth J, Noppornpitak J, Ward H, Magee P, Al Baz A, Kajendirarajah U, Kapadia S, Vlasblom J, Valluri M, Green J, Seifer V, Quirbach M, Rennie O, Kelley E, Masjedi N, Lord C, Szego MJ, Zawati MH, Lang M, Strug LJ, Marshall CR, Costain G, Calli K, Iaboni A, Yusuf A, Ambrozewicz P, Gallagher L, Amaral DG, Brian J, Elsabbagh M, Georgiades S, Messinger DS, Ozonoff S, Sebat J, Sjaarda C, Smith IM, Szatmari P, Zwaigenbaum L, Kushki A, Frazier TW, Vorstman JAS, Fakhro KA, Fernandez BA, Lewis MES, Weksberg R, Fiume M, Yuen RKC, Anagnostou E, Sondheimer N, Glazer D, Hartley DM, Scherer SW. Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell 2022; 185:4409-4427.e18. [PMID: 36368308 PMCID: PMC10726699 DOI: 10.1016/j.cell.2022.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/30/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Ada J S Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; CGEn, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Cherith Somerville
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mona Abdi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ny Hoang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thanuja Selvanayagam
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Nicole Deflaux
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Melissa Geng
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Bates
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Edwin J Young
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Qiliang Ding
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clarrisa A Bradley
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Annabel Rutherford
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vernie Aguda
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Beverly Apresto
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nan Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sachin Desai
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyan Du
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Matthew L Y Fong
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sanjeev Pullenayegum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kozue Samler
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ting Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Tara Paton
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olivia Rennie
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elizabeth Kelley
- Department of Psychology, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada
| | - Nina Masjedi
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Catherine Lord
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael J Szego
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Ma'n H Zawati
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Michael Lang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Lisa J Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Costain
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kristina Calli
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Afiqah Yusuf
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Patricia Ambrozewicz
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Child, Youth and Family Services, The Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - David G Amaral
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jessica Brian
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Mayada Elsabbagh
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3K7, Canada
| | | | - Sally Ozonoff
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jonathan Sebat
- Department of Psychiatry and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada; Queen's Genomics Lab at Ongwanada, Queen's University, Kingston, ON K7M 8A6, Canada
| | - Isabel M Smith
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada; IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Azadeh Kushki
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Thomas W Frazier
- Autism Speaks, Princeton, NJ 08540, USA; Department of Psychology, John Carroll University, Cleveland, OH 44118, USA
| | - Jacob A S Vorstman
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Bridget A Fernandez
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Ryan K C Yuen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Evdokia Anagnostou
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Neal Sondheimer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, Toronto, ON M5G 0A4, Canada.
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Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation. Proc Natl Acad Sci U S A 2022; 119:e2212417119. [PMID: 36322731 PMCID: PMC9659340 DOI: 10.1073/pnas.2212417119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial dysfunction can be associated with a range of clinical manifestations. Here, we report a family with a complex phenotype including combinations of connective tissue, neurological, and metabolic symptoms that were passed on to all surviving children. Analysis of the maternally inherited mtDNA revealed a novel genotype encompassing the haplogroup J - defining mitochondrial DNA (mtDNA) ND5 m.13708G>A (A458T) variant arising on the mtDNA haplogroup H7A background, an extremely rare combination. Analysis of transmitochondrial cybrids with the 13708A-H7 mtDNA revealed a lower mitochondrial respiration, increased reactive oxygen species production (mROS), and dysregulation of connective tissue gene expression. The mitochondrial dysfunction was exacerbated by histamine, explaining why all eight surviving children inherited the dysfunctional histidine decarboxylase allele (W327X) from the father. Thus, certain combinations of common mtDNA variants can cause mitochondrial dysfunction, mitochondrial dysfunction can affect extracellular matrix gene expression, and histamine-activated mROS production can augment the severity of mitochondrial dysfunction. Most important, we have identified a previously unreported genetic cause of mitochondrial disorder arising from the incompatibility of common, nonpathogenic mtDNA variants.
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Caporali L, Fiorini C, Palombo F, Romagnoli M, Baccari F, Zenesini C, Visconti P, Posar A, Scaduto MC, Ormanbekova D, Battaglia A, Tancredi R, Cameli C, Viggiano M, Olivieri A, Torroni A, Maestrini E, Rochat MJ, Bacchelli E, Carelli V, Maresca A. Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder. Front Genet 2022; 13:953762. [PMID: 36419830 PMCID: PMC9676943 DOI: 10.3389/fgene.2022.953762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD includes different genetic models, from monogenic transmission at one end, to polygenic risk given by thousands of common variants with small effects at the other end. The mitochondrial DNA (mtDNA) was also proposed as a genetic modifier for ASD, mostly focusing on maternal mtDNA, since the paternal mitogenome is not transmitted to offspring. We extensively studied the potential contribution of mtDNA in ASD pathogenesis and risk through deep next generation sequencing and quantitative PCR in a cohort of 98 families. While the maternally-inherited mtDNA did not seem to predispose to ASD, neither for haplogroups nor for the presence of pathogenic mutations, an unexpected influence of paternal mtDNA, apparently centered on haplogroup U, came from the Italian families extrapolated from the test cohort (n = 74) when compared to the control population. However, this result was not replicated in an independent Italian cohort of 127 families and it is likely due to the elevated paternal age at time of conception. In addition, ASD probands showed a reduced mtDNA content when compared to their unaffected siblings. Multivariable regression analyses indicated that variants with 15%-5% heteroplasmy in probands are associated to a greater severity of ASD based on ADOS-2 criteria, whereas paternal super-haplogroups H and JT were associated with milder phenotypes. In conclusion, our results suggest that the mtDNA impacts on ASD, significantly modifying the phenotypic expression in the Italian population. The unexpected finding of protection induced by paternal mitogenome in term of severity may derive from a role of mtDNA in influencing the accumulation of nuclear de novo mutations or epigenetic alterations in fathers' germinal cells, affecting the neurodevelopment in the offspring. This result remains preliminary and needs further confirmation in independent cohorts of larger size. If confirmed, it potentially opens a different perspective on how paternal non-inherited mtDNA may predispose or modulate other complex diseases.
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Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Baccari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali Jane Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma Diagnostica Funzionale Neuroradiologica, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
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47
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Sen A, Cox RT. Loss of Drosophila Clueless differentially affects the mitochondrial proteome compared to loss of Sod2 and Pink1. Front Physiol 2022; 13:1004099. [DOI: 10.3389/fphys.2022.1004099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria contain their own DNA, mitochondrial DNA, which encodes thirteen proteins. However, mitochondria require thousands of proteins encoded in the nucleus to carry out their many functions. Identifying the definitive mitochondrial proteome has been challenging as methods isolating mitochondrial proteins differ and different tissues and organisms may have specialized proteomes. Mitochondrial diseases arising from single gene mutations in nucleus encoded genes could affect the mitochondrial proteome, but deciphering which effects are due to loss of specific pathways or to accumulated general mitochondrial damage is difficult. To identify specific versus general effects, we have taken advantage of mutations in three Drosophila genes, clueless, Sod2, and Pink1, which are required for mitochondrial function through different pathways. We measured changes in each mutant’s mitochondrial proteome using quantitative tandem mass tag mass spectrometry. Our analysis identified protein classes that are unique to each mutant and those shared between them, suggesting that some changes in the mitochondrial proteome are due to general mitochondrial damage whereas others are gene specific. For example, clueless mutants had the greatest number of less and more abundant mitochondrial proteins whereas loss of all three genes increased stress and metabolism proteins. This study is the first to directly compare in vivo steady state levels of mitochondrial proteins by examining loss of three pathways critical for mitochondrial function. These data could be useful to understand disease etiology, and how mutations in genes critical for mitochondrial function cause specific mitochondrial proteomic changes as opposed to changes due to generalized mitochondrial damage.
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48
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Mitochondrial DNA population variation is not associated with Alzheimer's in the Japanese population: A consistent finding across global populations. PLoS One 2022; 17:e0276169. [PMID: 36264923 PMCID: PMC9584534 DOI: 10.1371/journal.pone.0276169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
Several mitochondrial DNA (mtDNA) haplogroup association studies have suggested that common mtDNA variants are associated with multifactorial diseases, including Alzheimer’s disease (AD). However, such studies have also produced conflicting results. A new mtDNA association model, the ‘variant load model’ (VLM), has been applied to multiple disease phenotypes. Application of the VLM in a 2017 study failed to find different variant loads in AD patients compared to controls, in two cohorts of European origin. The study also suggested a lower variant load in healthy elderly individuals, but could offer no replicate cohort to support this observation. Here, the VLM is applied to Japanese mtDNA sequences; in doing so, we explored the role of mtDNA variation in AD and ageing in a different global population. Consistent with the previous findings using the VLM in two populations of European origin, we found no evidence for an association between rarer, non-haplogroup associated variation and the development of AD. However, the result in the context of ageing that suggested those with fewer mildly deleterious mutations might undergo healthier ageing, was not replicated. In contrast to our previous study, our present results suggest that those living to advanced old age may harbour more mildly deleterious mtDNA variations. Importantly our analysis showed this finding is not primarily being driven by many rare population variants dispersed across the mtDNA, but by a few more frequent variants with high MutPred scores. It is suggested the variants in question do not exert a mildly deleterious effect in their most frequent haplogroup context.
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49
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Keraite I, Becker P, Canevazzi D, Frias-López C, Dabad M, Tonda-Hernandez R, Paramonov I, Ingham MJ, Brun-Heath I, Leno J, Abulí A, Garcia-Arumí E, Heath SC, Gut M, Gut IG. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nat Commun 2022; 13:5902. [PMID: 36202811 PMCID: PMC9537161 DOI: 10.1038/s41467-022-33530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. Accurate analysis of mitochondrial DNA is important for mitochondrial disease clinical research and diagnostics. Here, authors present a method using Cas9 cleavage, nanopore sequencing and a custom pipeline to identify pathogenic variants, deletions and accurately quantify heteroplasmy to below 1%.
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Affiliation(s)
- Ieva Keraite
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Becker
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Qiagen, Hilden, Germany
| | - Davide Canevazzi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cristina Frias-López
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raúl Tonda-Hernandez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthew John Ingham
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Jordi Leno
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Research Group on Neuromuscular and Mitochondrial Disorders, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Simon Charles Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
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50
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Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis. Eur J Hum Genet 2022; 30:1121-1131. [PMID: 35970915 PMCID: PMC9553973 DOI: 10.1038/s41431-022-01162-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/01/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.
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