1
|
Gupta V, Jolly B, Bhoyar RC, Divakar MK, Jain A, Mishra A, Senthivel V, Imran M, Scaria V, Sivasubbu S. Spectrum of rare and common mitochondrial DNA variations from 1029 whole genomes of self-declared healthy individuals from India. Comput Biol Chem 2024; 112:108118. [PMID: 38878606 DOI: 10.1016/j.compbiolchem.2024.108118] [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: 09/08/2023] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 09/13/2024]
Abstract
Mitochondrial disorders are a class of heterogeneous disorders caused by genetic variations in the mitochondrial genome (mtDNA) as well as the nuclear genome. The spectrum of mtDNA variants remains unexplored in the Indian population. In the present study, we have cataloged 2689 high confidence single nucleotide variants, small insertions and deletions in mtDNA in 1029 healthy Indian individuals. We found a major proportion (76.5 %) of the variants being rare (AF<=0.005) in the studied population. Intriguingly, we found two 'confirmed' pathogenic variants (m.1555 A>G and m.14484 T>C) with a frequency of ∼1 in 250 individuals in our dataset. The high carrier frequency underscores the need for screening of the mtDNA pathogenic mutations in newborns in India. Interestingly, our analysis also revealed 202 variants in our dataset which have been 'reported' in disease cases as per the MITOMAP database. Additionally, we found the frequency of haplogroup M (52.2 %) to be the highest among all the 18 top-level haplogroups found in our dataset. In comparison to the global population datasets, 20 unique mtDNA variants are found in the Indian population. We hope the whole genome sequencing based compendium of mtDNA variants along with their allele frequencies and heteroplasmy levels in the Indian population will drive additional genome scale studies for mtDNA. Furthermore, the identification of clinically relevant variants in our dataset will aid in better clinical interpretation of the variants in mitochondrial disorders.
Collapse
Affiliation(s)
- Vishu Gupta
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
2
|
Daca-Roszak P, Fiedorowicz J, Jankowski M, Ciesielka M, Teresiński G, Lipska-Zietkiewicz B, Zietkiewicz E, Grzybowski T, Skonieczna K. The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems. J Appl Genet 2024; 65:559-563. [PMID: 38110828 PMCID: PMC11310223 DOI: 10.1007/s13353-023-00821-4] [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: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.
Collapse
Affiliation(s)
| | - Joanna Fiedorowicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Animal Physiology, Biochemistry and Biostructure, Poznan University of Life Science, Poznan, Poland
| | - Maciej Jankowski
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Teresiński
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Beata Lipska-Zietkiewicz
- Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland; Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Zietkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
| |
Collapse
|
3
|
Gao F, Schon KR, Vandrovcova J, Wilson L, Hanna MG, Çavdarlı B, Heckmann J, Chinnery PF, Horvath R. Mitochondrial DNA disorders in neuromuscular diseases in diverse populations. Ann Clin Transl Neurol 2024. [PMID: 39095335 DOI: 10.1002/acn3.52141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Neuromuscular features are common in mitochondrial DNA (mtDNA) disorders. The genetic architecture of mtDNA disorders in diverse populations is poorly understood. We analysed mtDNA variants from whole-exome sequencing data in neuromuscular patients from South Africa, Brazil, India, Turkey and Zambia. In 998 individuals, there were two definite diagnoses, two possible diagnoses and eight secondary findings. Surprisingly, common pathogenic mtDNA variants found in people of European ancestry were very rare. Whole-exome or -genome sequencing from undiagnosed patients with neuromuscular symptoms should be re-analysed for mtDNA variants, but the landscape of pathogenic mtDNA variants differs around the world.
Collapse
Affiliation(s)
- Fei Gao
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Katherine R Schon
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Jana Vandrovcova
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Lindsay Wilson
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michael G Hanna
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Büşranur Çavdarlı
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Jeannine Heckmann
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, Groote Schuur Hospital, Cape Town, South Africa
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Huq A, Thompson B, Winship I. Clinical application of whole genome sequencing in young onset dementia: challenges and opportunities. Expert Rev Mol Diagn 2024; 24:659-675. [PMID: 39135326 DOI: 10.1080/14737159.2024.2388765] [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: 04/25/2024] [Accepted: 08/01/2024] [Indexed: 08/30/2024]
Abstract
INTRODUCTION Young onset dementia (YOD) by its nature is difficult to diagnose. Despite involvement of multidisciplinary neurogenetics services, patients with YOD and their families face significant diagnostic delays. Genetic testing for people with YOD currently involves a staggered, iterative approach. There is currently no optimal single genetic investigation that simultaneously identifies the different genetic variants resulting in YOD. AREAS COVERED This review discusses the advances in clinical genomic testing for people with YOD. Whole genome sequencing (WGS) can be employed as a 'one stop shop' genomic test for YOD. In addition to single nucleotide variants, WGS can reliably detect structural variants, short tandem repeat expansions, mitochondrial genetic variants as well as capture single nucleotide polymorphisms for the calculation of polygenic risk scores. EXPERT OPINION WGS, when used as the initial genetic test, can enhance the likelihood of a precision diagnosis and curtail the time taken to reach this. Finding a clinical diagnosis using WGS can reduce invasive and expensive investigations and could be cost effective. These advances need to be balanced against the limitations of the technology and the genetic counseling needs for these vulnerable patients and their families.
Collapse
Affiliation(s)
- Aamira Huq
- Department of Genomic Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Bryony Thompson
- Department of Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
5
|
Stawiński P, Płoski R. Genebe.net: Implementation and validation of an automatic ACMG variant pathogenicity criteria assignment. Clin Genet 2024; 106:119-126. [PMID: 38440907 DOI: 10.1111/cge.14516] [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: 11/17/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
We present GeneBe, an online platform streamlining the automated application of American College of Medical Genetics and Genomics (ACMG), Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP) criteria for assessment of pathogenicity of genetic variants. GeneBe utilizes automated algorithms that evaluate 17 criteria from 28, closely aligning with current guidelines and leveraging data from diverse sources, including ClinVar. The user-friendly web interface enables manual refinement of assignments for specific criteria based on site-collected data. Our algorithm demonstrates a high correlation (r = 0.90) of assigned pathogenicity scores compared to expert assessments from the ClinGen Evidence Repository and substantial concordance with ClinVar verdict assignments (κ = 0.69). Comparative analysis with other published tools reveals that GeneBe performs similarly to VarSome while being superior over TAPES and InterVar. In contrast to some other tools, GeneBe's web implementation is tracker-free and third-party request-free, safeguarding user privacy. Additionally, GeneBe offers an Application Programming Interface (API) for enhanced flexibility and integration into existing workflows and is provided free of charge for research purposes. GeneBe is available at https://genebe.net.
Collapse
Affiliation(s)
- Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
6
|
Sun L, Ren Y, Ma Y, Zhu Y, Wu Y, Wang S, Nie L, Xiao H, Jiang Y, Wang F. A de novo novel variant in the MT-TD gene is associated with prominent extra-neurologic manifestations. Clin Genet 2024. [PMID: 39056263 DOI: 10.1111/cge.14594] [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: 05/25/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Defects in the mitochondrial tRNA genes cause a group of highly clinically and genetically heterogeneous disorders, which poses a challenge for clinical identification and genetic diagnosis. Here, we present a pre-school boy with a novel MT-TD variant m.7560T>C at the heteroplasmy level of 76.53% in blood, 93.34% in urine sediments, and absent in the healthy mother's blood and urine. Besides convulsions, brain magnetic resonance imaging abnormalities and high plasma lactate, the boy presented with the prominent extra-neurologic phenotype including steroid-resistant nephrotic syndrome associated with focal segmental glomerulosclerosis characterized by abnormal mitochondria in podocytes, cortical blindness, and pancreatitis. To our knowledge, this is the unique case with MT-TD m.7560T>C-related multi-organ impairments, which expands the phenotypic and mutational spectrum of primary mitochondrial diseases.
Collapse
Affiliation(s)
- Liuyu Sun
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Yali Ren
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Yinan Ma
- Experimental Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Ying Zhu
- Department of Medical Imaging, Peking University First Hospital, Beijing, People's Republic of China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Suxia Wang
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Lin Nie
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| |
Collapse
|
7
|
Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 2024; 187:3904-3918.e8. [PMID: 38851187 DOI: 10.1016/j.cell.2024.05.022] [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: 08/26/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.
Collapse
Affiliation(s)
| | | | - Valdís B Guðmundsdóttir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Kamran Guity
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland.
| |
Collapse
|
8
|
Houge G, Bratland E, Aukrust I, Tveten K, Žukauskaitė G, Sansovic I, Brea-Fernández AJ, Mayer K, Paakkola T, McKenna C, Wright W, Markovic MK, Lildballe DL, Konecny M, Smol T, Alhopuro P, Gouttenoire EA, Obeid K, Todorova A, Jankovic M, Lubieniecka JM, Stojiljkovic M, Buisine MP, Haukanes BI, Lorans M, Roomere H, Petit FM, Haanpää MK, Beneteau C, Pérez B, Plaseska-Karanfilska D, Rath M, Fuhrmann N, Ferreira BI, Stephanou C, Sjursen W, Maver A, Rouzier C, Chirita-Emandi A, Gonçalves J, Kuek WCD, Broly M, Haer-Wigman L, Thong MK, Tae SK, Hyblova M, den Dunnen JT, Laner A. Comparison of the ABC and ACMG systems for variant classification. Eur J Hum Genet 2024; 32:858-863. [PMID: 38778080 PMCID: PMC11219933 DOI: 10.1038/s41431-024-01617-8] [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: 12/19/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
Collapse
Affiliation(s)
- Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Eirik Bratland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Gabrielė Žukauskaitė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ivona Sansovic
- Department of Medical and Laboratory Genetics, Endocrinology and Diabetology, Childrens' Hospital Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBERER), Santiago de Compostela, Spain
| | - Karin Mayer
- Center for Human Genetics and Laboratory Diagnostics, MVZ Martinsried GmbH, Martinsried, Germany
| | - Teija Paakkola
- Nordlab Wellbeing Service Group, Genetics Laboratory, Oulu, Finland
| | - Caoimhe McKenna
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - William Wright
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - Milica Keckarevic Markovic
- Center for Applied and Forensic Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dorte L Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Konecny
- Laboratory of Genomic Medicine, GHC GENETICS SK, Bratislava, Slovakia
- Department of Biology, Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Thomas Smol
- Institut de Genetique Medicale-CHU Lille, Lille, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Katharina Obeid
- Molecular Diagnostics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory "Genica" and Genome Center Bulgaria, Sofia, Bulgaria
| | - Milena Jankovic
- Neurology Clinic UCCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marie-Pierre Buisine
- Molecular Oncogenetics, Department of Biochemistry and Molecular Biology, Lille University Hospital, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, CANTHER, Lille, France
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marie Lorans
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Hanno Roomere
- Department of laboratory genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - François M Petit
- Department of Oncopharmacology, Centre Antoine Lacassagne, Nice, France
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland
| | - Claire Beneteau
- CHU Bordeaux, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Belén Pérez
- Genetics Department of CEDEM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Matthias Rath
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bibiana I Ferreira
- GENELAB by ABC, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Coralea Stephanou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, Ljubljana, Slovenia
| | - Cécile Rouzier
- Department of Medical Genetics, National Centre for Mitocondrial Diseases, CHU de NICE, Université Côte d'Azur, Nice, France
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Adela Chirita-Emandi
- Department of Microscopic Morphology Genetics Discipline, Center of Genomic Medicine, "Victor Babes" University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - João Gonçalves
- Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Wei Cheng David Kuek
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Kent Ridge, Singapore
| | - Martin Broly
- Laboratory of Rare and Autoinflammatory Genetic Diseases, Department of Genetics-LBM, Montpellier University Hospital, Montpellier, France
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Meow-Keong Thong
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok-Kun Tae
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ) München, Munich, Germany
| |
Collapse
|
9
|
Carey AR, Miller NR, Cui H, Allis K, Balog A, Bai R, Vernon HJ. Myopathy and Ophthalmologic Abnormalities in Association With Multiple Skeletal Muscle Mitochondrial DNA Deletions. J Neuroophthalmol 2024; 44:247-252. [PMID: 37665646 DOI: 10.1097/wno.0000000000001984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
BACKGROUND Establishing a molecular diagnosis of mitochondrial diseases due to pathogenic mitochondrial DNA (mtDNA) variants can be difficult because of varying levels of tissue heteroplasmy, and identifying these variants is important for clinical management. Here, we present clinical and molecular findings in 8 adult patients with classical features of mitochondrial ophthalmologic and/or muscle disease and multiple mtDNA deletions isolated to muscle. METHODS The patients were identified via a retrospective review of patients seen in both a tertiary ophthalmology center and a genetics clinic with a clinical diagnosis of chronic progressive external ophthalmoplegia, optic nerve abnormalities, and/or mitochondrial myopathy. Age at onset of symptoms ranged from 18 to 61 years. Ocular manifestations included bilateral optic neuropathy in one patient, bilateral optic disc cupping without optic neuropathy in 2 patients, ptosis in 4 patients, and ocular motility deficits in 2 patients. Five patients had generalized weakness. RESULTS Pathogenic variants in mtDNA were not found in the blood or buccal sample from any patient, but 7 of 8 patients had multiple mtDNA deletions identified in muscle tissue. One patient had a single mtDNA deletion identified in the muscle. Heteroplasmy was less than 15% for all of the identified deletions, with the exception of one deletion that had a heteroplasmy of 50%-60%. None of the patients were found to have a nuclear gene variant known to be associated with mitochondrial DNA maintenance. CONCLUSIONS mtDNA deletions were identified in adult patients with ophthalmologic and/or musle abnormalities and may underlie their clinical presentations.
Collapse
Affiliation(s)
- Andrew R Carey
- Neuro-Ophthalmology Division (ARC, NRM), Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; GeneDx (HC, KA, AB, RB), Gaithersburg, Maryland; and Department of Genetic Medicine (HJV), Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | | |
Collapse
|
10
|
Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [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: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
Collapse
Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Zhuang X, Ye R, Zhou Y, Cheng MY, Cui H, Wang L, Zhang S, Wang S, Cui Y, Zhang W. Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma. Genome Med 2024; 16:50. [PMID: 38566210 PMCID: PMC10985887 DOI: 10.1186/s13073-024-01319-2] [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: 05/23/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Mitochondria play essential roles in tumorigenesis; however, little is known about the contribution of mitochondrial DNA (mtDNA) to esophageal squamous cell carcinoma (ESCC). Whole-genome sequencing (WGS) is by far the most efficient technology to fully characterize the molecular features of mtDNA; however, due to the high redundancy and heterogeneity of mtDNA in regular WGS data, methods for mtDNA analysis are far from satisfactory. METHODS Here, we developed a likelihood-based method dMTLV to identify low-heteroplasmic mtDNA variants. In addition, we described fNUMT, which can simultaneously detect non-reference nuclear sequences of mitochondrial origin (non-ref NUMTs) and their derived artifacts. Using these new methods, we explored the contribution of mtDNA to ESCC utilizing the multi-omics data of 663 paired tumor-normal samples. RESULTS dMTLV outperformed the existing methods in sensitivity without sacrificing specificity. The verification using Nanopore long-read sequencing data showed that fNUMT has superior specificity and more accurate breakpoint identification than the current methods. Leveraging the new method, we identified a significant association between the ESCC overall survival and the ratio of mtDNA copy number of paired tumor-normal samples, which could be potentially explained by the differential expression of genes enriched in pathways related to metabolism, DNA damage repair, and cell cycle checkpoint. Additionally, we observed that the expression of CBWD1 was downregulated by the non-ref NUMTs inserted into its intron region, which might provide precursor conditions for the tumor cells to adapt to a hypoxic environment. Moreover, we identified a strong positive relationship between the number of mtDNA truncating mutations and the contribution of signatures linked to tumorigenesis and treatment response. CONCLUSIONS Our new frameworks promote the characterization of mtDNA features, which enables the elucidation of the landscapes and roles of mtDNA in ESCC essential for extending the current understanding of ESCC etiology. dMTLV and fNUMT are freely available from https://github.com/sunnyzxh/dMTLV and https://github.com/sunnyzxh/fNUMT , respectively.
Collapse
Affiliation(s)
- Xuehan Zhuang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Rui Ye
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yong Zhou
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Matthew Yibo Cheng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Heyang Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Longlong Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Shuangping Zhang
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shubin Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Yongping Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
| | - Weimin Zhang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100142, China.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Koleilat A, Poling GL, Schimmenti LA, Hasadsri L. The Importance of Mitochondrial Disease Testing in Young Adults With New Onset Sensorineural Hearing Loss. Ear Hear 2024; 45:517-521. [PMID: 37930162 DOI: 10.1097/aud.0000000000001442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
OBJECTIVES Sensorineural hearing loss (SNHL) occurs commonly as part of mitochondriopathies and varies in severity and onset. In this study, we characterized hearing with specific consideration for hearing loss as a potential early indicator of mitochondrial disease (MD). We hypothesize that genetic testing at the earliest detection of SNHL may lead to an earlier MD diagnosis. DESIGN We reviewed the clinical and audiometric data of 49 patients undergoing genetic testing for MD. RESULTS One-third of individuals with molecularly confirmed MD presented with SNHL. On average, patients had hearing loss at least 10 years before genetic testing. The collective audiometric profile includes mild to moderate SNHL at lower frequencies and moderate SNHL at 2 kHz and higher frequencies. CONCLUSIONS This study suggests that screening for SNHL could be an early indicator of MD. We propose that the audiometric profile for those with a MD diagnosis may have clinical triage utility.
Collapse
Affiliation(s)
- Alaa Koleilat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gayla L Poling
- Division of Audiology, Department of Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
15
|
Pi Y, Huang Z, Xu X, Zhang H, Jin M, Zhang S, Lin G, Hu L. Increases in computationally predicted deleterious variants of unknown significance and sperm mtDNA copy numbers may be associated with semen quality. Andrology 2024; 12:585-598. [PMID: 37622679 DOI: 10.1111/andr.13521] [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: 01/10/2023] [Revised: 06/24/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Mitochondria are essential for sperm motility because they provide the energy required for the movement. Changes in sperm mtDNA, such as point mutations, large-scale deletions, or copy number variations, may interfere with ATP production and reduce sperm motility. However, it is not clear if changes in mtDNA are linked to semen quality. OBJECTIVES To explore the association between sperm mitochondrial DNA (mtDNA) changes and semen quality. MATERIALS AND METHODS Sixty-five oligo and/or astheno and/or terato patients (O/A/T) patients and 41 controls were recruited from couples undergoing assisted reproduction. Semen and blood samples were collected from the same individual on the day of oocyte retrieval to extract, isolate and purify mtDNA for next-generation sequencing. mtDNA copy numbers were assessed in 64 patient and 39 control sperm DNA samples using quantitative real-time PCR. The 4977 bp deletion was assessed in 20 patient and 20 control sperm DNA samples using polymerase chain reaction. RESULTS The mtDNA of patients was more likely to carry pathogenic variants or variants of unknown significance (VUSs) (P = 0.091) with higher heteroplasmy levels (P < 0.05) than that of controls. Interestingly, 33.85% of O/A/T patients (22 out of 65) lacked unique variants in their spermatozoa. but presented an exceptionally high mtDNA copy number (P < 0.0001). Moreover, we observed a decrease in the heteroplasmy level of common mtDNA variants shared by somatic and gamete cells (P < 0.0001) and the emergence of a very large number of de novo mtDNA variants with low-level heteroplasmy in spermatozoa. DISCUSSION AND CONCLUSION The increases in the number of computationally predicted deleterious VUS and mtDNA copies in spermatozoa may be associated with semen quality. Exposure to environmental mutation pressure that causes novel mtDNA variants with low-level heteroplasmy may occur during spermatogenesis. Furthermore, when a certain harmful threshold is reached, male germ cells may degrade mtDNA with mutations and replicate the correct mtDNA sequence to maintain the mitochondrial function in spermatozoa.
Collapse
Affiliation(s)
- Yuze Pi
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhuo Huang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Xilin Xu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Huan Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Miao Jin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Shuoping Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation base of Development and Carcinogenesis, Changsha, Hunan, China
| |
Collapse
|
16
|
Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [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: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
Collapse
Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
| |
Collapse
|
17
|
Nogueira C, Pereira C, Silva L, Laranjeira M, Lopes A, Neiva R, Rodrigues E, Campos T, Martins E, Bandeira A, Coelho M, Magalhães M, Damásio J, Gaspar A, Janeiro P, Gomes AL, Ferreira AC, Jacinto S, Vieira JP, Diogo L, Santos H, Mendonça C, Vilarinho L. The genetic landscape of mitochondrial diseases in the next-generation sequencing era: a Portuguese cohort study. Front Cell Dev Biol 2024; 12:1331351. [PMID: 38465286 PMCID: PMC10920333 DOI: 10.3389/fcell.2024.1331351] [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: 10/31/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: Rare disorders that are genetically and clinically heterogeneous, such as mitochondrial diseases (MDs), have a challenging diagnosis. Nuclear genes codify most proteins involved in mitochondrial biogenesis, despite all mitochondria having their own DNA. The development of next-generation sequencing (NGS) technologies has revolutionized the understanding of many genes involved in the pathogenesis of MDs. In this new genetic era, using the NGS approach, we aimed to identify the genetic etiology for a suspected MD in a cohort of 450 Portuguese patients. Methods: We examined 450 patients using a combined NGS strategy, starting with the analysis of a targeted mitochondrial panel of 213 nuclear genes, and then proceeding to analyze the whole mitochondrial DNA. Results and Discussion: In this study, we identified disease-related variants in 134 (30%) analyzed patients, 88 with nuclear DNA (nDNA) and 46 with mitochondrial DNA (mtDNA) variants, most of them being pediatric patients (66%), of which 77% were identified in nDNA and 23% in mtDNA. The molecular analysis of this cohort revealed 72 already described pathogenic and 20 novel, probably pathogenic, variants, as well as 62 variants of unknown significance. For this cohort of patients with suspected MDs, the use of a customized gene panel provided a molecular diagnosis in a timely and cost-effective manner. Patients who cannot be diagnosed after this initial approach will be further selected for whole-exome sequencing. Conclusion: As a national laboratory for the study and research of MDs, we demonstrated the power of NGS to achieve a molecular etiology, expanding the mutational spectrum and proposing accurate genetic counseling in this group of heterogeneous diseases without therapeutic options.
Collapse
Affiliation(s)
- C. Nogueira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - C. Pereira
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - L. Silva
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Mateus Laranjeira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - A. Lopes
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - R. Neiva
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - E. Rodrigues
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - T. Campos
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - E. Martins
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - A. Bandeira
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Coelho
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Magalhães
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - J. Damásio
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - A. Gaspar
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - P Janeiro
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. Levy Gomes
- Neurology Department, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. C. Ferreira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - S. Jacinto
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - J. P. Vieira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - L. Diogo
- Inherited Metabolic Diseases Reference Centre, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - H. Santos
- Inherited Metabolic Diseases Reference Centre, Vila Nova de Gaia Hospital Centre, Vila Nova de Gaia, Portugal
| | - C. Mendonça
- Pediatric Department, Faro Hospital and University Centre, Faro, Portugal
| | - L. Vilarinho
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Kim SJ, Joo E, Park J, Seol CA, Lee JE. Genetic evaluation using next-generation sequencing of children with short stature: a single tertiary-center experience. Ann Pediatr Endocrinol Metab 2024; 29:38-45. [PMID: 38461804 PMCID: PMC10925784 DOI: 10.6065/apem.2346036.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2024] Open
Abstract
PURPOSE We used next-generation sequencing (NGS) to investigate the genetic causes of suspected genetic short stature in 37 patients, and we describe their phenotypes and various genetic spectra. METHODS We reviewed the medical records of 50 patients who underwent genetic testing using NGS for suspected genetic short stature from June 2019 to December 2022. Patients with short stature caused by nongenetic factors or common chromosomal abnormalities were excluded. Thirty-seven patients from 35 families were enrolled in this study. We administered one of three genetic tests (2 targeted panel tests or whole exome sequencing) to patients according to their phenotypes. RESULTS Clinical and molecular diagnoses were confirmed in 15 of the 37 patients, for an overall diagnostic yield of 40.5%. Fifteen pathogenic/likely pathogenic variants were identified in 13 genes (ACAN, ANKRD11, ARID1B, CEP152, COL10A1, COL1A2, EXT1, FGFR3, NIPBL, NRAS, PTPN11, SHOX, SLC16A2). The diagnostic rate was highest in patients who were small for their gestational age (7 of 11, 63.6%). CONCLUSION Genetic evaluation using NGS can be helpful in patients with suspected genetic short stature who have clinical and genetic heterogeneity. Further studies are needed to develop patient selection algorithms and panels containing growth-related genes.
Collapse
Affiliation(s)
- Su Jin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| | - Eunyoung Joo
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Jisun Park
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | | | - Ji-Eun Lee
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| |
Collapse
|
20
|
Wang X, Li H, Luo H, Zou Y, Li H, Qin Y, Song J. Evaluating ClinGen variant curation expert panels' application of PVS1 code. Eur J Med Genet 2024; 67:104909. [PMID: 38199457 DOI: 10.1016/j.ejmg.2024.104909] [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: 04/17/2023] [Revised: 08/02/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines articulates that the effects of certain types of variants on gene function can often be seen as a complete absence of the gene product by leading to a lack of transcription or nonsense-mediated decay(NMD). However, detailed information considering different types of loss of function(LOF) variants, refined steps assimilating details concerning location of variant, changes in strength levels, NMD boundary, or any additional information pointing to a true null effect, were all left to expert judgement. As part of its Clinical Genome Resource (ClinGen) initiative, Variant Curation Expert Panels (VCEPs) are designated to make gene/disease-centric specifications in accordance with the ACMG/AMP guidelines, including a more detailed definition of what constitutes an appropriate LOF evidence. Our goal was to evaluate the current LOF guidelines developed by the VCEPs and analyse the prior curated variants concerning the PVS1 criteria, bringing people occupied in genetic data analysis a comprehensive understanding of this code. METHODS Our study evaluated 7 VCEPs for their LOF criteria (PVS1). Subsequently, we assessed the predictive criteria by considering the underlying disease mechanism, protein transcript, and variant types delineated. Then, we meticulously curated the LOF evidence referenced by each VCEP in their preliminary variant classification, thereby scrutinizing the recommendations put forth by VCEPs and their application in the interpretation of the aforementioned predictive criteria. Based on these, an extensive curation of evidence summary considering PVS1 applied by VCEPs according to their classification of pilot variants for the purpose of analyzing VCEP criteria specifications and their use in the understanding of LOF was conducted. RESULTS We observed in this article that the VCEPs discussed followed the majority of Sequence Variant Interpretation (SVI) recommendations concerning the application of this LOF criteria, except for some disease/gene specific considerations. We highlighted the wide range of PVS1 strength levels approved by VCEP, reflecting the diversity of evidence for each variants type. In addition, we observed substantial differences in the approach used to determine relative strengths for different types of null variants and in the attitude towards these principles concerning variant location, NMD and influence to protein function between VCEPs. CONCLUSIONS It is difficult to understand the intricacies of the predictive data(PVS1), which often requires expert-level knowledge of disease/gene. The VCEP criteria specifications for the predictive evidence play an important role in making it more accessible for the curators to apply the predictive data by providing details concerning this complex criteria. Despite this, we believe there is a need for more guidance on standardizing this process and ensuring consistency in the application of this predictive evidence.
Collapse
Affiliation(s)
- Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, 339 Liuting St, Ningbo City, Zhejiang Province, China
| | - Haiyan Luo
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Haoxian Li
- Center of Medical Genetics, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong, China
| | - Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China.
| |
Collapse
|
21
|
Chin HL, Lai PS, Tay SKH. A clinical approach to diagnosis and management of mitochondrial myopathies. Neurotherapeutics 2024; 21:e00304. [PMID: 38241155 PMCID: PMC10903095 DOI: 10.1016/j.neurot.2023.11.001] [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: 08/30/2023] [Accepted: 11/11/2023] [Indexed: 01/21/2024] Open
Abstract
This paper provides an overview of the different types of mitochondrial myopathies (MM), associated phenotypes, genotypes as well as a practical clinical approach towards disease diagnosis, surveillance, and management. nDNA-related MM are more common in pediatric-onset disease whilst mtDNA-related MMs are more frequent in adults. Genotype-phenotype correlation in MM is challenging due to clinical and genetic heterogeneity. The multisystemic nature of many MMs adds to the diagnostic challenge. Diagnostic approaches utilizing genetic sequencing with next generation sequencing approaches such as gene panel, exome and genome sequencing are available. This aids molecular diagnosis, heteroplasmy detection in MM patients and furthers knowledge of known mitochondrial genes. Precise disease diagnosis can end the diagnostic odyssey for patients, avoid unnecessary testing, provide prognosis, facilitate anticipatory management, and enable access to available therapies or clinical trials. Adjunctive tests such as functional and exercise testing could aid surveillance of MM patients. Management requires a multi-disciplinary approach, systemic screening for comorbidities, cofactor supplementation, avoidance of substances that inhibit the respiratory chain and exercise training. This update of the current understanding on MMs provides practical perspectives on current diagnostic and management approaches for this complex group of disorders.
Collapse
Affiliation(s)
- Hui-Lin Chin
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stacey Kiat Hong Tay
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore.
| |
Collapse
|
22
|
Shen L, Falk MJ, Gai X. MSeqDR Quick-Mitome (QM): Combining Phenotype-Guided Variant Interpretation and Machine Learning Classifiers to Aid Primary Mitochondrial Disease Genetic Diagnosis. Curr Protoc 2024; 4:e955. [PMID: 38284225 PMCID: PMC11046528 DOI: 10.1002/cpz1.955] [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] [Indexed: 01/30/2024]
Abstract
The international Mitochondrial Disease Sequence Data Resource Consortium (MSeqDR) Quick-Mitome (QM) is a web-based platform enabling automated variant interpretation of whole-exome sequencing (WES) datasets for the genetic diagnosis of primary mitochondrial diseases (PMD). Designed specifically to address the unique dual genome nature of PMD etiologies, QM includes features for both nuclear and mitochondrial DNA (mtDNA) genome analysis. QM requires VCF variant lists, HPO ID clinical phenotypes, and pedigree files for multiple-sample VCF inputs. QM maps phenotypes to HPO terms before analysis. QM analysis requires 2 to 20 min for 100,000 variants on an 8-vCPU AWS server using Exomiser's "PASS_ONLY" mode for nuclear variants. QM ranks variants based on allele frequency, phenotype-gene association, functional impact, and inheritance mode. Variants are further annotated with multiple data sources such as OMIM, ClinVar, dbNSFP, gnoMAD, MITOMAP, and MSeqDR. In addition to standard Exomiser results, QM generates an Analysis Report and QM Integrated Report with add-on mtDNA-specific analyses, including haplogroup prediction with Phy-Mer, heteroplasmy calculation, and mvTool annotations. We developed the Mitochondrial Disease Variant (MDV) classifier using XGBoost to predict variant pathogenicity for PMD. The MDV classifier was trained on >120 features and performance benchmarking showed that it correctly classified >98% of nuclear gene variants as being pathogenic or benign, and predicted PMD-causing variants with 94% precision. The MSeqDR QM server is an open-access resource for phenotype-driven dual-genome analyses for PMD diagnosis by the global mitochondrial disease community. It is publicly available for non-commercial, non-clinical research use at https://mseqdr.org/quickmitome.php. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Standardizing clinical phenotypes into human phenotype ontology (HPO) terms as the phenotype input for Quick-Mitome (QM) Basic Protocol 2: Prepare the pedigree input for multiple-sample VCF Basic Protocol 3: Quick-Mitome (QM) analysis Basic Protocol 4: Reviewing and understanding the QM Integrated Report and Analysis Report.
Collapse
Affiliation(s)
- Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, California, USA
| |
Collapse
|
23
|
Olimpio C, Paramonov I, Matalonga L, Laurie S, Schon K, Polavarapu K, Kirschner J, Schara-Schmidt U, Lochmüller H, Chinnery PF, Horvath R. Increased Diagnostic Yield by Reanalysis of Whole Exome Sequencing Data in Mitochondrial Disease. J Neuromuscul Dis 2024; 11:767-775. [PMID: 38759022 PMCID: PMC11307028 DOI: 10.3233/jnd-240020] [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] [Accepted: 04/16/2024] [Indexed: 05/19/2024]
Abstract
Background The genetic diagnosis of mitochondrial disorders is complicated by its genetic and phenotypic complexity. Next generation sequencing techniques have much improved the diagnostic yield for these conditions. A cohort of individuals with multiple respiratory chain deficiencies, reported in the literature 10 years ago, had a diagnostic rate of 60% by whole exome sequencing (WES) but 40% remained undiagnosed. Objective We aimed to identify a genetic diagnosis by reanalysis of the WES data for the undiagnosed arm of this 10-year-old cohort of patients with suspected mitochondrial disorders. Methods The WES data was transferred and processed by the RD-Connect Genome-Phenome Analysis Platform (GPAP) using their standardized pipeline. Variant prioritisation was carried out on the RD-Connect GPAP. Results Singleton WES data from 14 individuals was reanalysed. We identified a possible or likely genetic diagnosis in 8 patients (8/14, 57%). The variants identified were in a combination of mitochondrial DNA (n = 1, MT-TN), nuclear encoded mitochondrial genes (n = 2, PDHA1, and SUCLA2) and nuclear genes associated with nonmitochondrial disorders (n = 5, PNPLA2, CDC40, NBAS and SLC7A7). Variants in both the NBAS and CDC40 genes were established as disease causing after the original cohort was published. We increased the diagnostic yield for the original cohort by 15% without generating any further genomic data. Conclusions In the era of multiomics we highlight that reanalysis of existing WES data is a valid tool for generating additional diagnosis in patients with suspected mitochondrial disease, particularly when more time has passed to allow for new bioinformatic pipelines to emerge, for the development of new tools in variant interpretation aiding in reclassification of variants and the expansion of scientific knowledge on additional genes.
Collapse
Affiliation(s)
- Catarina Olimpio
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ida Paramonov
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | | | - Steven Laurie
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | - Katherine Schon
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kiran Polavarapu
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Center for Neuromuscular Disorders, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Essen, Germany
| | - Hanns Lochmüller
- Centro Nacional de Análisis Genómico, Barcelona, Spain
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Patrick F. Chinnery
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| |
Collapse
|
24
|
Huang S, Wu Z, Wang T, Yu R, Song Z, Wang H. MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases. Hum Genomics 2023; 17:108. [PMID: 38012712 PMCID: PMC10683248 DOI: 10.1186/s40246-023-00557-6] [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: 02/26/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Recent advances in next-generation sequencing (NGS) technology have greatly accelerated the need for efficient annotation to accurately interpret clinically relevant genetic variants in human diseases. Therefore, it is crucial to develop appropriate analytical tools to improve the interpretation of disease variants. Given the unique genetic characteristics of mitochondria, including haplogroup, heteroplasmy, and maternal inheritance, we developed a suite of variant analysis toolkits specifically designed for primary mitochondrial diseases: the Mitochondrial Missense Variant Annotation Tool (MmisAT) and the Mitochondrial Missense Variant Pathogenicity Predictor (MmisP). MmisAT can handle protein-coding variants from both nuclear DNA and mtDNA and generate 349 annotation types across six categories. It processes 4.78 million variant data in 76 min, making it a valuable resource for clinical and research applications. Additionally, MmisP provides pathogenicity scores to predict the pathogenicity of genetic variations in mitochondrial disease. It has been validated using cross-validation and external datasets and demonstrated higher overall discriminant accuracy with a receiver operating characteristic (ROC) curve area under the curve (AUC) of 0.94, outperforming existing pathogenicity predictors. In conclusion, the MmisAT is an efficient tool that greatly facilitates the process of variant annotation, expanding the scope of variant annotation information. Furthermore, the development of MmisP provides valuable insights into the creation of disease-specific, phenotype-specific, and even gene-specific predictors of pathogenicity, further advancing our understanding of specific fields.
Collapse
Affiliation(s)
- Shuangshuang Huang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhaoyu Wu
- Department of Clinical Laboratory, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tong Wang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Rui Yu
- Department of Ophthalmology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhijian Song
- OrigiMed, 5th Floor, Building 3, No.115 Xin Jun Huan Road, Minhang District, Shanghai, China.
| | - Hao Wang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| |
Collapse
|
25
|
Li Y, Wu Y, Xu R, Guo J, Quan F, Zhang Y, Huang D, Pei Y, Gao H, Liu W, Liu J, Zhang Z, Deng R, Shi J, Zhang K. In vivo imaging of mitochondrial DNA mutations using an integrated nano Cas12a sensor. Nat Commun 2023; 14:7722. [PMID: 38001092 PMCID: PMC10673915 DOI: 10.1038/s41467-023-43552-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) play critical roles in many human diseases. In vivo visualization of cells bearing mtDNA mutations is important for resolving the complexity of these diseases, which remains challenging. Here we develop an integrated nano Cas12a sensor (InCasor) and show its utility for efficient imaging of mtDNA mutations in live cells and tumor-bearing mouse models. We co-deliver Cas12a/crRNA, fluorophore-quencher reporters and Mg2+ into mitochondria. This process enables the activation of Cas12a's trans-cleavage by targeting mtDNA, which efficiently cleave reporters to generate fluorescent signals for robustly sensing and reporting single-nucleotide variations (SNVs) in cells. Since engineered crRNA significantly increase Cas12a's sensitivity to mismatches in mtDNA, we can identify tumor tissue and metastases by visualizing cells with mutant mtDNAs in vivo using InCasor. This CRISPR imaging nanoprobe holds potential for applications in mtDNA mutation-related basic research, diagnostics and gene therapies.
Collapse
Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Ru Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Jialing Guo
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongyuan Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Di Huang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Yiran Pei
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Hua Gao
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Wei Liu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China.
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China.
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
26
|
Meshrkey F, Scheulin KM, Littlejohn CM, Stabach J, Saikia B, Thorat V, Huang Y, LaFramboise T, Lesnefsky EJ, Rao RR, West FD, Iyer S. Induced pluripotent stem cells derived from patients carrying mitochondrial mutations exhibit altered bioenergetics and aberrant differentiation potential. Stem Cell Res Ther 2023; 14:320. [PMID: 37936209 PMCID: PMC10631039 DOI: 10.1186/s13287-023-03546-7] [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: 05/17/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Human mitochondrial DNA mutations are associated with common to rare mitochondrial disorders, which are multisystemic with complex clinical pathologies. The pathologies of these diseases are poorly understood and have no FDA-approved treatments leading to symptom management. Leigh syndrome (LS) is a pediatric mitochondrial disorder that affects the central nervous system during early development and causes death in infancy. Since there are no adequate models for understanding the rapid fatality associated with LS, human-induced pluripotent stem cell (hiPSC) technology has been recognized as a useful approach to generate patient-specific stem cells for disease modeling and understanding the origins of the phenotype. METHODS hiPSCs were generated from control BJ and four disease fibroblast lines using a cocktail of non-modified reprogramming and immune evasion mRNAs and microRNAs. Expression of hiPSC-associated intracellular and cell surface markers was identified by immunofluorescence and flow cytometry. Karyotyping of hiPSCs was performed with cytogenetic analysis. Sanger and next-generation sequencing were used to detect and quantify the mutation in all hiPSCs. The mitochondrial respiration ability and glycolytic function were measured by the Seahorse Bioscience XFe96 extracellular flux analyzer. RESULTS Reprogrammed hiPSCs expressed pluripotent stem cell markers including transcription factors POU5F1, NANOG and SOX2 and cell surface markers SSEA4, TRA-1-60 and TRA-1-81 at the protein level. Sanger sequencing analysis confirmed the presence of mutations in all reprogrammed hiPSCs. Next-generation sequencing demonstrated the variable presence of mutant mtDNA in reprogrammed hiPSCs. Cytogenetic analyses confirmed the presence of normal karyotype in all reprogrammed hiPSCs. Patient-derived hiPSCs demonstrated decreased maximal mitochondrial respiration, while mitochondrial ATP production was not significantly different between the control and disease hiPSCs. In line with low maximal respiration, the spare respiratory capacity was lower in all the disease hiPSCs. The hiPSCs also demonstrated neural and cardiac differentiation potential. CONCLUSION Overall, the hiPSCs exhibited variable mitochondrial dysfunction that may alter their differentiation potential and provide key insights into clinically relevant developmental perturbations.
Collapse
Affiliation(s)
- Fibi Meshrkey
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
- Department of Histology and Cell Biology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Kelly M Scheulin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Christopher M Littlejohn
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Joshua Stabach
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Bibhuti Saikia
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward J Lesnefsky
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
- Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, VA, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA
- Division of Cardiology, Department of Internal Medicine, Pauley Heart Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Raj R Rao
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Franklin D West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA.
| |
Collapse
|
27
|
Viering DH, Vermeltfoort L, Bindels RJ, Deinum J, de Baaij JH. Electrolyte Disorders in Mitochondrial Cytopathies: A Systematic Review. J Am Soc Nephrol 2023; 34:1875-1888. [PMID: 37678265 PMCID: PMC10631606 DOI: 10.1681/asn.0000000000000224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
SIGNIFICANCE STATEMENT Several recent studies identified mitochondrial mutations in patients with Gitelman or Fanconi syndrome. Mitochondrial cytopathies are generally not considered in the diagnostic workup of patients with electrolyte disorders. In this systematic review, we investigated the presence of electrolyte disorders in patients with mitochondrial cytopathies to determine the relevance of mitochondrial mutation screening in this population. Our analysis demonstrates that electrolyte disorders are commonly reported in mitochondrial cytopathies, often as presenting symptoms. Consequently, more clinical attention should be raised for mitochondrial disease as cause for disturbances in electrolyte homeostasis. Further prospective cohort studies are required to determine the exact prevalence of electrolyte disorders in mitochondrial cytopathies. BACKGROUND Electrolyte reabsorption in the kidney has a high energy demand. Proximal and distal tubular epithelial cells have a high mitochondrial density for energy release. Recently, electrolyte disorders have been reported as the primary presentation of some mitochondrial cytopathies. However, the prevalence and the pathophysiology of electrolyte disturbances in mitochondrial disease are unknown. Therefore, we systematically investigated electrolyte disorders in patients with mitochondrial cytopathies. METHODS We searched PubMed, Embase, and Google Scholar for articles on genetically confirmed mitochondrial disease in patients for whom at least one electrolyte is reported. Patients with a known second genetic anomaly were excluded. We evaluated 214 case series and reports (362 patients) as well as nine observational studies. Joanna Briggs Institute criteria were used to evaluate the quality of included studies. RESULTS Of 362 reported patients, 289 had an electrolyte disorder, with it being the presenting or main symptom in 38 patients. The average number of different electrolyte abnormalities per patient ranged from 2.4 to 1.0, depending on genotype. Patients with mitochondrial DNA structural variants seemed most affected. Reported pathophysiologic mechanisms included renal tubulopathies and hormonal, gastrointestinal, and iatrogenic causes. CONCLUSIONS Mitochondrial diseases should be considered in the evaluation of unexplained electrolyte disorders. Furthermore, clinicians should be aware of electrolyte abnormalities in patients with mitochondrial disease.
Collapse
Affiliation(s)
- Daan H.H.M. Viering
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lars Vermeltfoort
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - René J.M. Bindels
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen H.F. de Baaij
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
28
|
Takeda Y, Hyslop L, Choudhary M, Robertson F, Pyle A, Wilson I, Santibanez‐Koref M, Turnbull D, Herbert M, Hudson G. Feasibility and impact of haplogroup matching for mitochondrial replacement treatment. EMBO Rep 2023; 24:e54540. [PMID: 37589175 PMCID: PMC10561356 DOI: 10.15252/embr.202154540] [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: 12/17/2021] [Revised: 07/03/2023] [Accepted: 07/26/2023] [Indexed: 08/18/2023] Open
Abstract
Mitochondrial replacement technology (MRT) aims to reduce the risk of serious disease in children born to women who carry pathogenic mitochondrial DNA (mtDNA) variants. By transplanting nuclear genomes from eggs of an affected woman to enucleated eggs from an unaffected donor, MRT creates new combinations of nuclear and mtDNA. Based on sets of shared sequence variants, mtDNA is classified into ~30 haplogroups. Haplogroup matching between egg donors and women undergoing MRT has been proposed as a means of reducing mtDNA sequence divergence between them. Here we investigate the potential effect of mtDNA haplogroup matching on clinical delivery of MRT and on mtDNA sequence divergence between donor/recipient pairs. Our findings indicate that haplogroup matching would limit the availability of egg donors such that women belonging to rare haplogroups may have to wait > 4 years for treatment. Moreover, we find that intra-haplogroup sequence variation is frequently within the range observed between randomly matched mtDNA pairs. We conclude that haplogroup matching would restrict the availability of MRT, without necessarily reducing mtDNA sequence divergence between donor/recipient pairs.
Collapse
Affiliation(s)
- Yuko Takeda
- Wellcome Centre for Mitochondrial Research, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Louise Hyslop
- Newcastle Fertility Centre, Biomedicine West WingCentre for LifeNewcastle upon TyneUK
| | - Meenakshi Choudhary
- Newcastle Fertility Centre, Biomedicine West WingCentre for LifeNewcastle upon TyneUK
| | - Fiona Robertson
- Wellcome Centre for Mitochondrial ResearchInstitute of Clinical Translational Research, Newcastle UniversityNewcastle upon TyneUK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial ResearchInstitute of Clinical Translational Research, Newcastle UniversityNewcastle upon TyneUK
| | - Ian Wilson
- Biosciences Institute, Centre for LifeNewcastle upon TyneUK
| | | | - Douglass Turnbull
- Wellcome Centre for Mitochondrial ResearchInstitute of Clinical Translational Research, Newcastle UniversityNewcastle upon TyneUK
| | - Mary Herbert
- Wellcome Centre for Mitochondrial Research, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
- Newcastle Fertility Centre, Biomedicine West WingCentre for LifeNewcastle upon TyneUK
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery InstituteMonash UniversityMelbourneVICAustralia
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| |
Collapse
|
29
|
Grigalionienė K, Burnytė B, Ambrozaitytė L, Utkus A. Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease. Orphanet J Rare Dis 2023; 18:307. [PMID: 37784170 PMCID: PMC10544509 DOI: 10.1186/s13023-023-02921-0] [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: 04/25/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Mitochondrial Diseases (MDs) are a diverse group of neurometabolic disorders characterized by impaired mitochondrial oxidative phosphorylation and caused by pathogenic variants in more than 400 genes. The implementation of next-generation sequencing (NGS) technologies helps to increase the understanding of molecular basis and diagnostic yield of these conditions. The purpose of the study was to investigate diagnostic and genotypic spectrum in patients with suspected MD. The comprehensive analysis of mtDNA variants using Sanger sequencing was performed in the group of 83 unrelated individuals with clinically suspected mitochondrial disease. Additionally, targeted next generation sequencing or whole exome sequencing (WES) was performed for 30 patients of the study group. RESULTS The overall diagnostic rate was 21.7% for the patients with suspected MD, increasing to 36.7% in the group of patients where NGS methods were applied. Mitochondrial disease was confirmed in 11 patients (13.3%), including few classical mitochondrial syndromes (MELAS, MERRF, Leigh and Kearns-Sayre syndrome) caused by pathogenic mtDNA variants (8.4%) and MDs caused by pathogenic variants in five nDNA genes. Other neuromuscular diseases caused by pathogenic variants in seven nDNA genes, were confirmed in seven patients (23.3%). CONCLUSION The wide spectrum of identified rare mitochondrial or neurodevelopmental diseases proves that MD suspected patients would mostly benefit from an extensive genetic profiling allowing rapid diagnostics and improving the care of these patients.
Collapse
Affiliation(s)
- Kristina Grigalionienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania.
| | - Birutė Burnytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| |
Collapse
|
30
|
Si L, Wang Z, Li XY, Song Y, Yao T, Xu E, Wang X, Wang C. Novel mutations and molecular pathways identified in patients with brain iron accumulation disorders. Neurogenetics 2023; 24:231-241. [PMID: 37453004 DOI: 10.1007/s10048-023-00725-9] [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: 04/04/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Brain iron accumulation disorders (BIADs) are a group of diseases characterized by iron overload in deep gray matter nuclei, which is a common feature of neurodegenerative diseases. Although genetic factors have been reported to be one of the etiologies, much more details about the genetic background and molecular mechanism of BIADs remain unclear. This study aimed to illustrate the genetic characteristics of BIADs and clarify their molecular mechanisms. A total of 84 patients with BIADs were recruited from April 2018 to October 2022 at Xuanwu Hospital. Clinical characteristics including family history, consanguineous marriage history, and age at onset (AAO) were collected and assessed by two senior neurologists. Neuroimaging data were conducted for all the patients, including cranial magnetic resonance imaging (MRI) and susceptibility-weighted imaging (SWI). Whole-exome sequencing (WES) and capillary electrophoresis for detecting sequence mutation and trinucleotide repeat expansion, respectively, were conducted on all patients and part of their parents (whose samples were available). Variant pathogenicity was assessed according to the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP). The NBIA and NBIA-like genes with mutations were included for bioinformatic analysis, using Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genome (KEGG). GO annotation and KEGG pathway analysis were performed on Metascape platform. In the 84 patients, 30 (35.7%) were found to carry mutations, among which 20 carried non-dynamic mutations (missense, stop-gained, frameshift, inframe, and exonic deletion) and 10 carried repeat expansion mutations. Compared with sporadic cases, familial cases had more genetic variants (non-dynamic mutation: P=0.025, dynamic mutation: P=0.003). AAO was 27.85±10.42 years in cases with non-dynamic mutations, which was significantly younger than those without mutations (43.13±17.17, t=3.724, P<0.001) and those with repeated expansions (45.40±8.90, t=4.550, P<0.001). Bioinformatic analysis suggested that genes in lipid metabolism, autophagy, mitochondria regulation, and ferroptosis pathways are more likely to be involved in the pathogenesis of BIADs. This study broadens the genetic spectrum of BIADs and has important implications in genetic counselling and clinical diagnosis. Patients diagnosed as BIADs with early AAO and family history are more likely to carry mutations. Bioinformatic analysis provides new insights into the molecular pathogenesis of BIADs, which may shed lights on the therapeutic strategy for neurodegenerative diseases.
Collapse
Affiliation(s)
- Lianghao Si
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Zhanjun Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Xu-Ying Li
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Yang Song
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Tingyan Yao
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Erhe Xu
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Xianling Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Chaodong Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China.
| |
Collapse
|
31
|
McCormick EM, Keller K, Taylor JP, Coffey AJ, Shen L, Krotoski D, Harding B, Gai X, Falk MJ, Zolkipli-Cunningham Z, Rahman S. Expert Panel Curation of 113 Primary Mitochondrial Disease Genes for the Leigh Syndrome Spectrum. Ann Neurol 2023; 94:696-712. [PMID: 37255483 PMCID: PMC10763625 DOI: 10.1002/ana.26716] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Primary mitochondrial diseases (PMDs) are heterogeneous disorders caused by inherited mitochondrial dysfunction. Classically defined neuropathologically as subacute necrotizing encephalomyelopathy, Leigh syndrome spectrum (LSS) is the most frequent manifestation of PMD in children, but may also present in adults. A major challenge for accurate diagnosis of LSS in the genomic medicine era is establishing gene-disease relationships (GDRs) for this syndrome with >100 monogenic causes across both nuclear and mitochondrial genomes. METHODS The Clinical Genome Resource (ClinGen) Mitochondrial Disease Gene Curation Expert Panel (GCEP), comprising 40 international PMD experts, met monthly for 4 years to review GDRs for LSS. The GCEP standardized gene curation for LSS by refining the phenotypic definition, modifying the ClinGen Gene-Disease Clinical Validity Curation Framework to improve interpretation for LSS, and establishing a scoring rubric for LSS. RESULTS The GDR with LSS across the nuclear and mitochondrial genomes was classified as definitive for 31 of 114 GDRs curated (27%), moderate for 38 (33%), limited for 43 (38%), and disputed for 2 (2%). Ninety genes were associated with autosomal recessive inheritance, 16 were maternally inherited, 5 were autosomal dominant, and 3 were X-linked. INTERPRETATION GDRs for LSS were established for genes across both nuclear and mitochondrial genomes. Establishing these GDRs will allow accurate variant interpretation, expedite genetic diagnosis of LSS, and facilitate precision medicine, multisystem organ surveillance, recurrence risk counseling, reproductive choice, natural history studies, and determination of eligibility for interventional clinical trials. ANN NEUROL 2023;94:696-712.
Collapse
Affiliation(s)
- Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Kierstin Keller
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology, CHOP, Philadelphia, PA, USA
| | - Julie P. Taylor
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Alison J. Coffey
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Danuta Krotoski
- IDDB/NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Brian Harding
- Departments of Pathology and Lab Medicine (Neuropathology), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shamima Rahman
- Mitochondrial Research Group, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, and Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Petrović Pajić S, Suštar Habjan M, Brecelj J, Fakin A, Volk M, Maver A, Jezernik G, Peterlin B, Glavač D, Hawlina M, Jarc-Vidmar M. Leber Hereditary Optic Neuropathy in a Family of Carriers of MT-ND5 m.13042G>T (A236S) Novel Variant. J Neuroophthalmol 2023; 43:341-347. [PMID: 36897664 DOI: 10.1097/wno.0000000000001820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
BACKGROUND A Slovenian three-generation family with 3 individuals with bilateral optic neuropathy and 2 unaffected relatives with a novel homoplasmic missense variant m.13042G > T (A236S) in the ND5 gene is described. A detailed phenotype at initial diagnosis and a follow-up of bilateral optic neuropathy progression is presented for 2 affected individuals. METHODS A detailed phenotype analysis with clinical examination in the early and chronic phase with electrophysiology and OCT segmentation is presented. Genotype analysis with full mitochondrial genome sequencing was performed. RESULTS Two affected male individuals (maternal cousins) had a profound visual loss at an early age (11 and 20 years) with no recovery. The maternal grandmother exhibited bilateral optic atrophy with a history of visual loss at the age 58 years. The visual loss of both affected male individuals was characterized by centrocecal scotoma, abnormal color vision, abnormal PERG N95, and VEP. Later with disease progression, retinal nerve fiber layer thinning was observed on OCT. We observed no other extraocular clinical features. Mitochondrial sequencing identified a homoplasmic novel variant m.13042G > T (A236S) in the MT-ND5 gene, belonging to a haplogroup K1a. CONCLUSIONS Novel homoplasmic variant m.13042G > T (A236S) in the ND5 gene in our family was associated with Leber hereditary optic neuropathy-like phenotype. However, predicting the pathogenicity of a novel ultra-rare missense variant in the mitochondrial ND5 gene is challenging. Genetic counseling should consider genotypic and phenotypic heterogeneity, incomplete penetrance, haplogroup type, and tissue-specific thresholds.
Collapse
Affiliation(s)
- Sanja Petrović Pajić
- Eye Hospital (SPP, MJV, BSK, MS, JB, AF, MSH), University Medical Centre Ljubljana, Ljubljana, Slovenia; Clinic for Eye Diseases (SPP), Clinical Centre of Serbia, Belgrade, Serbia; Department of Molecular Genetics (DG), Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; Center for Human Genetics and Pharmacogenomics (GJ, DG), Faculty of Medicine, University of Maribor, Maribor, Slovenia; Clinical Institute of Genomic Medicine (MV, AM, BP), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Skonieczna K, Grzybowski T. Capability of the iSeq 100 sequencing system from Illumina to detect low-level substitutions in the human mitochondrial genome. Forensic Sci Int Genet 2023; 66:102912. [PMID: 37451073 DOI: 10.1016/j.fsigen.2023.102912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The significance of mtDNA heteroplasmy in forensic and medical genetics has increased recently because massively parallel sequencing (MPS) technologies enable more accurate and precise detection of minority nucleotide variants. Recent reports have shown that detection of low-level substitutions may depend on library preparation or sequencing protocol, and can vary for different MPS platforms. The MiSeq (Illumina) and Ion S5 (Thermo Fisher Scientific) are mainly used for heteroplasmy detection, but no data are available regarding the iSeq 100, an Illumina platform of the smallest throughput. Notably, unlike the other systems, the machine utilizes sequencing by synthesis one-channel chemistry to determine DNA sequences. Thus, it is important to verify the capability of the iSeq 100 system to determine mitochondrial haplotypes and detect heteroplasmic substitutions. In this study, previously determined entire mitochondrial genomes were sequenced with the iSeq 100 system. Each mitogenome was sequenced twice, giving approximately 2000x and 10,000x coverage. All homoplasmic mutations and minority variants above the 19 % level detected with the iSeq 100 system were also observed after dideoxy sequencing. Moreover, all heteroplasmic substitutions above the 2 % level were consistently detected with SBS one-channel chemistry. However, detection of low-level mtDNA variants may require additional, confirmatory experiments. In summary, the iSeq 100 system enables reproducible and accurate sequencing of human mitochondrial genomes. Detection of mtDNA minority variants depends on the laboratory protocol and sequencing platform used, but homoplasmic mutations and heteroplasmy above the 2 % level can be correctly detected with the iSeq 100 system.
Collapse
Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland.
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
| |
Collapse
|
37
|
Macken WL, Falabella M, Pizzamiglio C, Woodward CE, Scotchman E, Chitty LS, Polke JM, Bugiardini E, Hanna MG, Vandrovcova J, Chandler N, Labrum R, Pitceathly RDS. Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications. Expert Rev Mol Diagn 2023; 23:797-814. [PMID: 37642407 DOI: 10.1080/14737159.2023.2241365] [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: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. AREAS COVERED In this review, we briefly summarize the current state of the art in molecular diagnostics for mtDNA and consider the implications of improved whole genome sequencing (WGS), bioinformatic techniques, and the adoption of long-read sequencing, for PMD diagnostics. EXPERT OPINION We anticipate that the application of PCR-free WGS from blood DNA will increase in diagnostic laboratories, while for adults with myopathic presentations, WGS from muscle DNA may become more widespread. Improved bioinformatic strategies will enhance WGS data interrogation, with more accurate delineation of mtDNA and NUMTs (nuclear mitochondrial DNA segments) in WGS data, superior coverage uniformity, indirect measurement of mtDNA copy number, and more accurate interpretation of heteroplasmic large-scale rearrangements (LSRs). Separately, the adoption of diagnostic long-read sequencing could offer greater resolution of complex LSRs and the opportunity to phase heteroplasmic variants.
Collapse
Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James M Polke
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Natalie Chandler
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| |
Collapse
|
38
|
Frascarelli C, Zanetti N, Nasca A, Izzo R, Lamperti C, Lamantea E, Legati A, Ghezzi D. Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions. Front Genet 2023; 14:1089956. [PMID: 37456669 PMCID: PMC10344361 DOI: 10.3389/fgene.2023.1089956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Primary mitochondrial diseases are progressive genetic disorders affecting multiple organs and characterized by mitochondrial dysfunction. These disorders can be caused by mutations in nuclear genes coding proteins with mitochondrial localization or by genetic defects in the mitochondrial genome (mtDNA). The latter include point pathogenic variants and large-scale deletions/rearrangements. MtDNA molecules with the wild type or a variant sequence can exist together in a single cell, a condition known as mtDNA heteroplasmy. MtDNA single point mutations are typically detected by means of Next-Generation Sequencing (NGS) based on short reads which, however, are limited for the identification of structural mtDNA alterations. Recently, new NGS technologies based on long reads have been released, allowing to obtain sequences of several kilobases in length; this approach is suitable for detection of structural alterations affecting the mitochondrial genome. In the present work we illustrate the optimization of two sequencing protocols based on long-read Oxford Nanopore Technology to detect mtDNA structural alterations. This approach presents strong advantages in the analysis of mtDNA compared to both short-read NGS and traditional techniques, potentially becoming the method of choice for genetic studies on mtDNA.
Collapse
Affiliation(s)
- Chiara Frascarelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rossella Izzo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| |
Collapse
|
39
|
Florian K, Benet-Pagès A, Berner D, Teubert A, Eck S, Arnold N, Bauer P, Begemann M, Sturm M, Kleinle S, B. Haack T, Eggermann T. Quality assurance within the context of genome diagnostics (a german perspective). MED GENET-BERLIN 2023; 35:91-104. [PMID: 38840862 PMCID: PMC10842579 DOI: 10.1515/medgen-2023-2028] [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: 06/07/2024]
Abstract
The rapid and dynamic implementation of Next-Generation Sequencing (NGS)-based assays has revolutionized genetic testing, and in the near future, nearly all molecular alterations of the human genome will be diagnosable via massive parallel sequencing. While this progress will further corroborate the central role of human genetics in the multidisciplinary management of patients with genetic disorders, it must be accompanied by quality assurance measures in order to allow the safe and optimal use of knowledge ascertained from genome diagnostics. To achieve this, several valuable tools and guidelines have been developed to support the quality of genome diagnostics. In this paper, authors with experience in diverse aspects of genomic analysis summarize the current status of quality assurance in genome diagnostics, with the aim of facilitating further standardization and quality improvement in one of the core competencies of the field.
Collapse
Affiliation(s)
- Kraft Florian
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinAachenDeutschland
| | - Anna Benet-Pagès
- Institut für NeurogenomikHelmholtz Zentrum MünchenNeuherbergDeutschland
| | | | | | | | - Norbert Arnold
- Universitätsklinikum Schleswig-HolsteinZentrum für familiären Brust- und Eierstockkrebs; Klinik für Gynäkologie und GeburtshilfeKielDeutschland
| | | | - Matthias Begemann
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinAachenDeutschland
| | - Marc Sturm
- Universität TübingenInstitut für Medizinische Genetik und Angewandte GenomikTübingenDeutschland
| | | | - Tobias B. Haack
- Universität TübingenInstitut für Medizinische Genetik und Angewandte GenomikTübingenDeutschland
| | - Thomas Eggermann
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinPauwelsstr. 3052074AachenDeutschland
| |
Collapse
|
40
|
Whitmore L, McCauley M, Farrell JA, Stammnitz MR, Koda SA, Mashkour N, Summers V, Osborne T, Whilde J, Duffy DJ. Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA. Nat Ecol Evol 2023; 7:873-888. [PMID: 37188965 PMCID: PMC10250199 DOI: 10.1038/s41559-023-02056-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/29/2023] [Indexed: 05/17/2023]
Abstract
The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from 'wildlife' environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.
Collapse
Affiliation(s)
- Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - Mark McCauley
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Maximilian R Stammnitz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Samantha A Koda
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Victoria Summers
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Todd Osborne
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Jenny Whilde
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA.
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Dong J, Buradagunta CS, Zhang T, Spellman S, Bolon YT, DeZern AE, Gadalla SM, Deeg HJ, Nazha A, Cutler C, Cheng C, Urrutia R, Auer P, Saber W. Prognostic landscape of mitochondrial genome in myelodysplastic syndrome after stem-cell transplantation. J Hematol Oncol 2023; 16:21. [PMID: 36899395 PMCID: PMC9999628 DOI: 10.1186/s13045-023-01418-4] [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: 12/19/2022] [Accepted: 02/26/2023] [Indexed: 03/12/2023] Open
Abstract
Despite mitochondrial DNA (mtDNA) mutations are common events in cancer, their global frequency and clinical impact have not been comprehensively characterized in patients with myelodysplastic neoplasia (also known as myelodysplastic syndromes, MDS). Here we performed whole-genome sequencing (WGS) on samples obtained before allogenic hematopoietic cell transplantation (allo-HCT) from 494 patients with MDS who were enrolled in the Center for International Blood and Marrow Transplant Research. We evaluated the impact of mtDNA mutations on transplantation outcomes, including overall survival (OS), relapse, relapse-free survival (RFS), and transplant-related mortality (TRM). A random survival forest algorithm was applied to evaluate the prognostic performance of models that include mtDNA mutations alone and combined with MDS- and HCT-related clinical factors. A total of 2666 mtDNA mutations were identified, including 411 potential pathogenic variants. We found that overall, an increased number of mtDNA mutations was associated with inferior transplantation outcomes. Mutations in several frequently mutated mtDNA genes (e.g., MT-CYB and MT-ND5) were identified as independent predictors of OS, RFS, relapse and/or TRM after allo-HCT. Integration of mtDNA mutations into the models based on the Revised International Prognostic Scores (IPSS-R) and clinical factors related to MDS and allo-HCT could capture more prognostic information and significantly improve the prognostic stratification efforts. Our study represents the first WGS effort in MDS receiving allo-HCT and shows that there may be clinical utility of mtDNA variants to predict allo-HCT outcomes in combination with more standard clinical parameters.
Collapse
Affiliation(s)
- Jing Dong
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, HRC 5860, Milwaukee, WI, 53226, USA.
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA.
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Christopher Staffi Buradagunta
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, HRC 5860, Milwaukee, WI, 53226, USA
| | - Tao Zhang
- CIBMTR® (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program®/Be The Match®, Minneapolis, MN, USA
| | - Stephen Spellman
- CIBMTR® (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program®/Be The Match®, Minneapolis, MN, USA
| | - Yung-Tsi Bolon
- CIBMTR® (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program®/Be The Match®, Minneapolis, MN, USA
| | - Amy E DeZern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aziz Nazha
- Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Corey Cutler
- Stem Cell Transplantation and Cellular Therapy, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Raul Urrutia
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Hematology and Oncology, Department of Medicine, CIBMTR® (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI, 53226, USA
- Cancer Center Biostatistics Shared Resource, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wael Saber
- Division of Hematology and Oncology, Department of Medicine, CIBMTR® (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI, 53226, USA.
| |
Collapse
|
43
|
Buonfiglio PI, Menazzi S, Francipane L, Lotersztein V, Ferreiro V, Elgoyhen AB, Dalamón V. Mitochondrial DNA variants in a cohort from Argentina with suspected Leber's hereditary optic neuropathy (LHON). PLoS One 2023; 18:e0275703. [PMID: 36827238 PMCID: PMC9956067 DOI: 10.1371/journal.pone.0275703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
The present study investigates the spectrum and analysis of mitochondrial DNA (mtDNA) variants associated with Leber hereditary optic neuropathy (LHON) in an Argentinean cohort, analyzing 3 LHON-associated mitochondrial genes. In 32% of the cases, molecular confirmation of the diagnosis could be established, due to the identification of disease-causing variants. A total of 54 variants were observed in a cohort of 100 patients tested with direct sequencing analysis. The frequent causative mutations m.11778G>A in MT-ND4, m.3460G>A in MT-ND1, and m.14484T>C in MT-ND6 were identified in 28% of the cases of our cohort. Secondary mutations in this Argentinean LHON cohort were m.11253T>C p.Ile165Thr in MT-ND4, identified in three patients (3/100, 3%) and m.3395A>G p.Tyr30Cys in MT-ND1, in one of the patients studied (1%). This study shows, for the first time, the analysis of mtDNA variants in patients with a probable diagnosis of LHON in Argentina. Standard molecular methods are an effective first approach in order to achieve genetic diagnosis of the disease, leaving NGS tests for those patients with negative results.
Collapse
Affiliation(s)
- Paula I. Buonfiglio
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Menazzi
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Liliana Francipane
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Vanesa Lotersztein
- Servicio de Genética, Hospital Militar Central “Dr. Cosme Argerich”, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Ana Belén Elgoyhen
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
- Servicio de Genética, Hospital Militar Central “Dr. Cosme Argerich”, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio Genos, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
| | - Viviana Dalamón
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
44
|
Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
Collapse
Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| |
Collapse
|
45
|
Mavraki E, Labrum R, Sergeant K, Alston CL, Woodward C, Smith C, Knowles CVY, Patel Y, Hodsdon P, Baines JP, Blakely EL, Polke J, Taylor RW, Fratter C. Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. Eur J Hum Genet 2023; 31:148-163. [PMID: 36513735 PMCID: PMC9905091 DOI: 10.1038/s41431-022-01249-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Primary mitochondrial disease describes a diverse group of neuro-metabolic disorders characterised by impaired oxidative phosphorylation. Diagnosis is challenging; >350 genes, both nuclear and mitochondrial DNA (mtDNA) encoded, are known to cause mitochondrial disease, leading to all possible inheritance patterns and further complicated by heteroplasmy of the multicopy mitochondrial genome. Technological advances, particularly next-generation sequencing, have driven a shift in diagnostic practice from 'biopsy first' to genome-wide analyses of blood and/or urine DNA. This has led to the need for a reference framework for laboratories involved in mitochondrial genetic testing to facilitate a consistent high-quality service. In the United Kingdom, consensus guidelines have been prepared by a working group of Clinical Scientists from the NHS Highly Specialised Service followed by national laboratory consultation. These guidelines summarise current recommended technologies and methodologies for the analysis of mtDNA and nuclear-encoded genes in patients with suspected mitochondrial disease. Genetic testing strategies for diagnosis, family testing and reproductive options including prenatal diagnosis are outlined. Importantly, recommendations for the minimum levels of mtDNA testing for the most common referral reasons are included, as well as guidance on appropriate referrals and information on the minimal appropriate gene content of panels when analysing nuclear mitochondrial genes. Finally, variant interpretation and recommendations for reporting of results are discussed, focussing particularly on the challenges of interpreting and reporting mtDNA variants.
Collapse
Affiliation(s)
- Eleni Mavraki
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Robyn Labrum
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Kate Sergeant
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Charlotte L Alston
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Cathy Woodward
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Charlotte V Y Knowles
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yogen Patel
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Philip Hodsdon
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jack P Baines
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Emma L Blakely
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Robert W Taylor
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Andreeva NA, Murakhovskaya YK, Krylova TD, Tsygankova PG, Sheremet NL. [Rare pathogenic nucleotide variants of mitochondrial DNA associated with Leber's hereditary optic neuropathy]. Vestn Oftalmol 2023; 139:166-174. [PMID: 38235644 DOI: 10.17116/oftalma2023139061166] [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: 01/19/2024]
Abstract
Patients with Leber Hereditary Optic Neuropathy (LHON) in most cases have one of the three most common mutations: m.11778G>A in the ND4 gene, m.3460G>A in the ND1 gene, or m.14484T>C in the ND6 gene. According to the international Mitomap database, in addition to these three most common mutations, there are 16 other primary mutations that are even more rare. There are nucleotide substitutions that are classified as candidate or conditionally pathogenic mutations. Their involvement in the disease development is not proven due to insufficient research. Moreover, in many publications, the authors describe new primary and potential mitochondrial DNA mutations associated with LHON, which are not yet included in the genetic data bases. This makes it possible to expand the diagnostic spectrum during genetic testing in the future. The advancements in genetic diagnostic technologies allow confirmation of the clinical diagnosis of LHON. The importance of genetic verification of the disease is determined by the existing problem of differential diagnosis of hereditary optic neuropathies with optic neuropathies of a different origin.
Collapse
Affiliation(s)
- N A Andreeva
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - Yu K Murakhovskaya
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - T D Krylova
- Research Centre for Medical Genetics, Moscow, Russia
| | | | - N L Sheremet
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| |
Collapse
|
48
|
Liu H, Cai B, Gong R, Yang Y, Wang J, Zhou D, Yu M, Li Y. Impact of genetically predicted characterization of mitochondrial DNA quantity and quality on osteoarthritis. Front Genet 2023; 14:1130411. [PMID: 36911418 PMCID: PMC9998702 DOI: 10.3389/fgene.2023.1130411] [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: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
Background: Existing studies have indicated that mitochondrial dysfunction may contribute to osteoarthritis (OA) development. However, the causal association between mitochondrial DNA (mtDNA) characterization and OA has not been extensively explored. Methods: Two-sample Mendelian randomization was performed to calculate the impact of mitochondrial genomic variations on overall OA as well as site-specific OA, with multiple analytical methods inverse variance weighted (IVW), weighted median (WM), MR-Egger and MR-robust adjusted profile score (MR-RAPS). Results: Genetically determined mitochondrial heteroplasmy (MtHz) and mtDNA abundance were not causally associated with overall OA. In site-specific OA analyses, the causal effect of mtDNA abundance on other OA sites, including hip, knee, thumb, hand, and finger, had not been discovered. There was a suggestively protective effect of MtHz on knee OA IVW OR = 0.632, 95% CI: 0.425-0.939, p-value = 0.023. No causal association between MtHz and other different OA phenotypes was found. Conclusion: MtHz shows potential to be a novel therapeutic target and biomarker on knee OA development. However, the variation of mtDNA abundance was measured from leukocyte in blood and the levels of MtHz were from saliva samples rather than cartilage or synovial tissues. Genotyping samples from synovial and cartilage can be a focus to further exploration.
Collapse
Affiliation(s)
- Houpu Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Bingyue Cai
- Department of Epidemiology and Health Statistics, School of Public Health, Hangzhou Medical College, Hangzhou, China
| | | | - Ye Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Jing Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Dan Zhou
- Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, China.,Vanderbit Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Min Yu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yingjun Li
- Department of Epidemiology and Health Statistics, School of Public Health, Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
49
|
Skonieczna K, Ciesielka M, Teresiński G, Grzybowski T. Low-level point heteroplasmy detection in human mitogenomes amplified with different polymerases and sequenced on MiSeq FGx platform. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2023; 73:131-138. [PMID: 38186038 DOI: 10.4467/16891716amsik.23.011.18686] [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] [Indexed: 01/09/2024] Open
Abstract
Introduction Massively parallel sequencing of mitogenomes usually requires prior amplification. The PCR step may influence the quality of the data obtained, especially when low-level heteroplasmy detection is applied. Aim The aim of this study was to compare the reliability of two different DNA polymerases in detecting homoplasmic and heteroplasmic substitutions in human mitogenomes. Material and methods Mitogenomes of five samples were amplified with Long PCR Enzyme Mix from Fermentas or TaKaRa LA Taq DNA Polymerase from TaKaRa. Then, NexteraTM XT DNA libraries were sequenced on MiSeq FGx platform (Illumina). mtDNA substitutions were called for alternative variants above the 1% level. Results All homoplasmic substitutions detected in amplicons generated with polymerases studied here and sequenced on MiSeq FGx system were consistently identified as homoplasmies with alternative sequencing methods. TaKaRa LA Taq DNA Polymerase was found to be less accurate in low-level heteroplasmy detection than Long PCR Enzyme Mix enzyme as more false negative and false positive results were observed for minority variants called above the 1% level. Nevertheless, both PCR systems studied can be successfully used to detect authentic mtDNA substitutions, for which minority variants exceed the 3.61% level assuming at least 10,000x coverage and sequencing Nextera XT DNA libraries on MiSeq FGx machine. Conclusions The accuracy and sensitivity of point heteroplasmy detection with the MiSeq FGx instrument varies on polymerase used for mtDNA amplification. Therefore, it is recommended to validate the laboratory protocols used for mtDNA substitution detection prior to their implementation for the forensic or medical genetics purposes.
Collapse
Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | | | - Grzegorz Teresiński
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| |
Collapse
|
50
|
Mitochondrial Unfolded Protein Response and Integrated Stress Response as Promising Therapeutic Targets for Mitochondrial Diseases. Cells 2022; 12:cells12010020. [PMID: 36611815 PMCID: PMC9818186 DOI: 10.3390/cells12010020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/10/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The development and application of high-throughput omics technologies have enabled a more in-depth understanding of mitochondrial biosynthesis metabolism and the pathogenesis of mitochondrial diseases. In accordance with this, a host of new treatments for mitochondrial disease are emerging. As an essential pathway in maintaining mitochondrial proteostasis, the mitochondrial unfolded protein response (UPRmt) is not only of considerable significance for mitochondrial substance metabolism but also plays a fundamental role in the development of mitochondrial diseases. Furthermore, in mammals, the integrated stress response (ISR) and UPRmt are strongly coupled, functioning together to maintain mitochondrial function. Therefore, ISR and UPRmt show great application prospects in the treatment of mitochondrial diseases. In this review, we provide an overview of the molecular mechanisms of ISR and UPRmt and focus on them as potential targets for mitochondrial disease therapy.
Collapse
|