1
|
Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 DOI: 10.1042/bcj20230262] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
Collapse
Affiliation(s)
- Tiago M Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| |
Collapse
|
2
|
Lin Y, Wang J, Xu R, Xu Z, Wang Y, Pan S, Zhang Y, Tao Q, Zhao Y, Yan C, Cao Z, Ji K. HiFi long-read amplicon sequencing for full-spectrum variants of human mtDNA. BMC Genomics 2024; 25:538. [PMID: 38822239 PMCID: PMC11141058 DOI: 10.1186/s12864-024-10433-9] [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: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Mitochondrial diseases (MDs) can be caused by single nucleotide variants (SNVs) and structural variants (SVs) in the mitochondrial genome (mtDNA). Presently, identifying deletions in small to medium-sized fragments and accurately detecting low-percentage variants remains challenging due to the limitations of next-generation sequencing (NGS). METHODS In this study, we integrated targeted long-range polymerase chain reaction (LR-PCR) and PacBio HiFi sequencing to analyze 34 participants, including 28 patients and 6 controls. Of these, 17 samples were subjected to both targeted LR-PCR and to compare the mtDNA variant detection efficacy. RESULTS Among the 28 patients tested by long-read sequencing (LRS), 2 patients were found positive for the m.3243 A > G hotspot variant, and 20 patients exhibited single or multiple deletion variants with a proportion exceeding 4%. Comparison between the results of LRS and NGS revealed that both methods exhibited similar efficacy in detecting SNVs exceeding 5%. However, LRS outperformed NGS in detecting SNVs with a ratio below 5%. As for SVs, LRS identified single or multiple deletions in 13 out of 17 cases, whereas NGS only detected single deletions in 8 cases. Furthermore, deletions identified by LRS were validated by Sanger sequencing and quantified in single muscle fibers using real-time PCR. Notably, LRS also effectively and accurately identified secondary mtDNA deletions in idiopathic inflammatory myopathies (IIMs). CONCLUSIONS LRS outperforms NGS in detecting various types of SNVs and SVs in mtDNA, including those with low frequencies. Our research is a significant advancement in medical comprehension and will provide profound insights into genetics.
Collapse
Affiliation(s)
- Yan Lin
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jiayin Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ran Xu
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Zhe Xu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yifan Wang
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Shirang Pan
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Yan Zhang
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Qing Tao
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingdao, Shandong, 266035, China
- Brain Science Research Institute, Shandong University, Jinan, Shandong, 250012, China
| | - Zhenhua Cao
- GrandOmics Biosciences, No.56 Zhichun Road, Haidian District, Beijing, 100098, China.
| | - Kunqian Ji
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Department of Neurology, Qilu Hospital, Shandong University, No. 107 West Wenhua Road, Jinan, Shandong, 250012, China.
| |
Collapse
|
3
|
Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [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: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
Collapse
Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
| |
Collapse
|
4
|
Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 DOI: 10.1038/s41594-024-01225-6] [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: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
Collapse
Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
5
|
Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
Collapse
Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
| |
Collapse
|
6
|
Sprason C, Tucker T, Clancy D. MtDNA deletions and aging. FRONTIERS IN AGING 2024; 5:1359638. [PMID: 38425363 PMCID: PMC10902006 DOI: 10.3389/fragi.2024.1359638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
Aging is the major risk factor in most of the leading causes of mortality worldwide, yet its fundamental causes mostly remain unclear. One of the clear hallmarks of aging is mitochondrial dysfunction. Mitochondria are best known for their roles in cellular energy generation, but they are also critical biosynthetic and signaling organelles. They also undergo multiple changes with organismal age, including increased genetic errors in their independent, circular genome. A key group of studies looking at mice with increased mtDNA mutations showed that premature aging phenotypes correlated with increased deletions but not point mutations. This generated an interest in mitochondrial deletions as a potential fundamental cause of aging. However, subsequent studies in different models have yielded diverse results. This review summarizes the research on mitochondrial deletions in various organisms to understand their possible roles in causing aging while identifying the key complications in quantifying deletions across all models.
Collapse
Affiliation(s)
| | | | - David Clancy
- Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| |
Collapse
|
7
|
Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D. Structural basis for DNA proofreading. Nat Commun 2023; 14:8501. [PMID: 38151585 PMCID: PMC10752894 DOI: 10.1038/s41467-023-44198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement of the mismatched base into the exonuclease site. Altogether, our findings suggest a conserved 'bolt-action' mechanism of proofreading based on iterative cycles of DNAP translocation without dissociation from the DNA, facilitating primer transfer between catalytic sites. Functional assays and mutagenesis corroborate this mechanism, connecting pathogenic mutations to crucial structural elements in proofreading steps.
Collapse
Affiliation(s)
- Gina Buchel
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Ashok R Nayak
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Karl Herbine
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Viktoriia O Sokolova
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Angelica Zamudio-Ochoa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.
| |
Collapse
|
8
|
Shammas MK, Nie Y, Gilsrud A, Huang X, Narendra DP, Chinnery PF. CHCHD10 mutations induce tissue-specific mitochondrial DNA deletions with a distinct signature. Hum Mol Genet 2023; 33:91-101. [PMID: 37815936 PMCID: PMC10729859 DOI: 10.1093/hmg/ddad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
Mutations affecting the mitochondrial intermembrane space protein CHCHD10 cause human disease, but it is not known why different amino acid substitutions cause markedly different clinical phenotypes, including amyotrophic lateral sclerosis-frontotemporal dementia, spinal muscular atrophy Jokela-type, isolated autosomal dominant mitochondrial myopathy and cardiomyopathy. CHCHD10 mutations have been associated with deletions of mitochondrial DNA (mtDNA deletions), raising the possibility that these explain the clinical variability. Here, we sequenced mtDNA obtained from hearts, skeletal muscle, livers and spinal cords of WT and Chchd10 G58R or S59L knockin mice to characterise the mtDNA deletion signatures of the two mutant lines. We found that the deletion levels were higher in G58R and S59L mice than in WT mice in some tissues depending on the Chchd10 genotype, and the deletion burden increased with age. Furthermore, we observed that the spinal cord was less prone to the development of mtDNA deletions than the other tissues examined. Finally, in addition to accelerating the rate of naturally occurring deletions, Chchd10 mutations also led to the accumulation of a novel set of deletions characterised by shorter direct repeats flanking the deletion breakpoints. Our results indicate that Chchd10 mutations in mice induce tissue-specific deletions which may also contribute to the clinical phenotype associated with these mutations in humans.
Collapse
Affiliation(s)
- Mario K Shammas
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Yu Nie
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Alexandra Gilsrud
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Xiaoping Huang
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Derek P Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| |
Collapse
|
9
|
Potapenko EY, Kashko ND, Knorre DA. Spontaneous Mutations in Saccharomyces cerevisiae mtDNA Increase Cell-to-Cell Variation in mtDNA Amount. Int J Mol Sci 2023; 24:17413. [PMID: 38139242 PMCID: PMC10743915 DOI: 10.3390/ijms242417413] [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: 10/18/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
In a eukaryotic cell, the ratio of mitochondrial DNA (mtDNA) to nuclear DNA (nDNA) is usually maintained within a specific range. This suggests the presence of a negative feedback loop mechanism preventing extensive mtDNA replication and depletion. However, the experimental data on this hypothetical mechanism are limited. In this study, we suggested that deletions in mtDNA, known to increase mtDNA abundance, can disrupt this mechanism, and thus, increase cell-to-cell variance in the mtDNA copy numbers. To test this, we generated Saccharomyces cerevisiae rho- strains with large deletions in the mtDNA and rho0 strains depleted of mtDNA. Given that mtDNA contributes to the total DNA content of exponentially growing yeast cells, we showed that it can be quantified in individual cells by flow cytometry using the DNA-intercalating fluorescent dye SYTOX green. We found that the rho- mutations increased both the levels and cell-to-cell heterogeneity in the total DNA content of G1 and G2/M yeast cells, with no association with the cell size. Furthermore, the depletion of mtDNA in both the rho+ and rho- strains significantly decreased the SYTOX green signal variance. The high cell-to-cell heterogeneity of the mtDNA amount in the rho- strains suggests that mtDNA copy number regulation relies on full-length mtDNA, whereas the rho- mtDNAs partially escape this regulation.
Collapse
Affiliation(s)
- Elena Yu. Potapenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Nataliia D. Kashko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A. Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
10
|
Serag M, Plutino M, Charles P, Azulay JP, Chaussenot A, Paquis-Flucklinger V, Ait-El-Mkadem Saadi S, Rouzier C. A Case Report of SYNE1 Deficiency-Mimicking Mitochondrial Disease and the Value of Pangenomic Investigations. Genes (Basel) 2023; 14:2154. [PMID: 38136976 PMCID: PMC10743207 DOI: 10.3390/genes14122154] [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: 11/08/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Mitochondrial disorders are characterized by a huge clinical, biochemical, and genetic heterogeneity, which poses significant diagnostic challenges. Several studies report that more than 50% of patients with suspected mitochondrial disease could have a non-mitochondrial disorder. Thus, only the identification of the causative pathogenic variant can confirm the diagnosis. Herein, we describe the diagnostic journey of a family suspected of having a mitochondrial disorder who were referred to our Genetics Department. The proband presented with the association of cerebellar ataxia, COX-negative fibers on muscle histology, and mtDNA deletions. Whole exome sequencing (WES), supplemented by a high-resolution array, comparative genomic hybridization (array-CGH), allowed us to identify two pathogenic variants in the non-mitochondrial SYNE1 gene. The proband and her affected sister were found to be compound heterozygous for a known nonsense variant (c.13258C>T, p.(Arg4420Ter)), and a large intragenic deletion that was predicted to result in a loss of function. To our knowledge, this is the first report of a large intragenic deletion of SYNE1 in patients with cerebellar ataxia (ARCA1). This report highlights the interest in a pangenomic approach to identify the genetic basis in heterogeneous neuromuscular patients with the possible cause of mitochondrial disease. Moreover, even rare copy number variations should be considered in patients with a phenotype suggestive of SYNE1 deficiency.
Collapse
Affiliation(s)
- Mounir Serag
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Morgane Plutino
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Perrine Charles
- Service de Génétique, La Pitié-Salpêtrière, AP-HP, 75610 Paris, France;
| | | | - Annabelle Chaussenot
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Véronique Paquis-Flucklinger
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Samira Ait-El-Mkadem Saadi
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Cécile Rouzier
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| |
Collapse
|
11
|
Granic A, Suetterlin K, Shavlakadze T, Grounds M, Sayer A. Hallmarks of ageing in human skeletal muscle and implications for understanding the pathophysiology of sarcopenia in women and men. Clin Sci (Lond) 2023; 137:1721-1751. [PMID: 37986616 PMCID: PMC10665130 DOI: 10.1042/cs20230319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Ageing is a complex biological process associated with increased morbidity and mortality. Nine classic, interdependent hallmarks of ageing have been proposed involving genetic and biochemical pathways that collectively influence ageing trajectories and susceptibility to pathology in humans. Ageing skeletal muscle undergoes profound morphological and physiological changes associated with loss of strength, mass, and function, a condition known as sarcopenia. The aetiology of sarcopenia is complex and whilst research in this area is growing rapidly, there is a relative paucity of human studies, particularly in older women. Here, we evaluate how the nine classic hallmarks of ageing: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication contribute to skeletal muscle ageing and the pathophysiology of sarcopenia. We also highlight five novel hallmarks of particular significance to skeletal muscle ageing: inflammation, neural dysfunction, extracellular matrix dysfunction, reduced vascular perfusion, and ionic dyshomeostasis, and discuss how the classic and novel hallmarks are interconnected. Their clinical relevance and translational potential are also considered.
Collapse
Affiliation(s)
- Antoneta Granic
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
| | - Karen Suetterlin
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, U.K
| | - Tea Shavlakadze
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, NY, U.S.A
| | - Miranda D. Grounds
- Department of Anatomy, Physiology and Human Biology, School of Human Sciences, the University of Western Australia, Perth, WA 6009, Australia
| | - Avan A. Sayer
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
| |
Collapse
|
12
|
Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
Collapse
Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| |
Collapse
|
13
|
Liu C, Le BH, Xu W, Yang CH, Chen YH, Zhao L. Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA. Nucleic Acids Res 2023; 51:e73. [PMID: 37293974 PMCID: PMC10359467 DOI: 10.1093/nar/gkad502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.
Collapse
Affiliation(s)
- Chaoxing Liu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon H Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ching-Hsin Yang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Yu Hsuan Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| |
Collapse
|
14
|
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
|
15
|
Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet 2023; 55:1198-1209. [PMID: 37386249 PMCID: PMC10548551 DOI: 10.1038/s41588-023-01433-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.
Collapse
Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yu-Hsin Hsieh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Kopal Garg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pauline Kautz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Technische Universität Berlin, Institute of Biotechnology, Berlin, Germany
| | - Lena Nitsch
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Samantha D Praktiknjo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Maschmeyer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jeffrey M Verboon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- Immunai, New York City, NY, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rhea Malhotra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumit Parikh
- Center for Pediatric Neurosciences, Mitochondrial Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lena Oevermann
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Johannes Schulte
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York City, NY, USA
- 10x Genomics, San Francisco, CA, USA
| | | | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
16
|
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
|
17
|
Vandiver AR, Hoang AN, Herbst A, Lee CC, Aiken JM, McKenzie D, Teitell MA, Timp W, Wanagat J. Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging. Aging Cell 2023; 22:e13842. [PMID: 37132288 PMCID: PMC10265159 DOI: 10.1111/acel.13842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next-generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency. We employed nanopore Cas9-targeted sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints. NCATS-mtDNA sequencing allows the identification of mtDNA deletions on a single-molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.
Collapse
Affiliation(s)
- Amy R. Vandiver
- Division of Dermatology, Department of MedicineUCLALos AngelesCaliforniaUSA
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
| | - Austin N. Hoang
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Allen Herbst
- US Geological Survey National Wildlife Health CenterMadisonWisconsinUSA
| | - Cathy C. Lee
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| | - Judd M. Aiken
- Department of Agricultural, Food and Nutritional SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Debbie McKenzie
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Michael A. Teitell
- Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pathology and Laboratory Medicine, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Bioengineering, California NanoSystems Institute, Broad Center for Regenerative Medicine and Stem Cell ResearchUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Department of Pediatrics, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer Center, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesCaliforniaUSA
| | - Winston Timp
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare SystemLos AngelesCaliforniaUSA
- Division of Geriatrics, Department of MedicineUCLALos AngelesCaliforniaUSA
| |
Collapse
|
18
|
Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Popadin K. Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biol 2023; 21:103. [PMID: 37158879 PMCID: PMC10166460 DOI: 10.1186/s12915-023-01606-1] [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: 06/17/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions. RESULTS By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging. CONCLUSIONS Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.
Collapse
Affiliation(s)
- Victor Shamanskiy
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Sergei Oreshkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia Ree
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Jonathan B Overdevest
- Department of Otolaryngology, Columbia University Irving Medical Center, New York, USA
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Australia
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Valerian Yurov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
- Department of Epileptology, University Hospital of Bonn, Bonn, Germany
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Georgii A Bazykin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia
| | - Jacques Fellay
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Masashi Tanaka
- Department for Health and Longevity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8636, Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Department of Clinical Laboratory, IMS Miyoshi General Hospital, Fujikubo, Miyoshi-Machi, Iruma, Saitama Prefecture, 974-3354-0041, Japan
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
19
|
Mitochondrial DNA Polymorphism in HV1 and HV2 Regions and 12S rDNA in Perimenopausal Hypertensive Women. Biomedicines 2023; 11:biomedicines11030823. [PMID: 36979802 PMCID: PMC10044999 DOI: 10.3390/biomedicines11030823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Estrogens enhance cellular mitochondrial activity. The diminution of female hormones during menopause may have an effect on the mitochondrial genome and the expression of mitochondrial proteins. Hence, oxidative stress and the pro-inflammatory state contribute to the formation of systemic illnesses including arterial hypertension (AH). This study aimed to determine the types and frequency of mutations in the mitochondrial DNA (mtDNA) nucleotide sequence in the hypervariable regions 1 and 2 (HV1 and HV2) and the 12S RNA coding sequence of the D-loop in postmenopausal women with hypertension. In our study, 100 women were investigated, 53 of whom were postmenopausal and 47 of whom were premenopausal (53.9 ± 3.7 years vs. 47.7 ± 4.2 years, respectively). Of those studied, 35 premenopausal and 40 postmenopausal women were diagnosed with AH. A medical checkup with 24 h monitoring of blood pressure (RR) and heart rate was undertaken (HR). The polymorphism of the D-loop and 12S rDNA region of mtDNA was examined. Changes in the nucleotide sequence of mtDNA were observed in 23% of the group of 100 women. The changes were identified in 91.3% of HV1 and HV2 regions, 60.9% of HV1 segments, 47.5% of HV2 regions, and 43.5% of 12S rDNA regions. The frequency of nucleotide sequence alterations in mtDNA was substantially higher in postmenopausal women (34%) than in premenopausal women (10.6%), p = 0.016. A higher frequency of changes in HV1 + HV2 sections in postmenopausal women (30.2%) compared to the premenopausal group (10.6%) was detected, p = 0.011. Only postmenopausal women were found to have modifications to the HV2 segment and the 12S rDNA region. After menopause, polymorphism in the mtDNA region was substantially more frequent in women with arterial hypertension than before menopause (p = 0.030; 37.5% vs. 11.5%). Comparable findings were observed in the HV2 and HV1 regions of the AH group (35% vs. 11.5%), p = 0.015, in the HV1 segment (25% vs. 11.5%), p = 0.529, and in the HV2 segment, 12S rDNA (25% vs. 0%). More than 80% of all changes in nucleotide sequence were homoplasmic. The mtDNA polymorphisms of the nucleotide sequence in the HV1 and HV2 regions, the HV2 region alone, and the 12S RNA coding sequence were associated with estrogen deficiency and a more severe course of arterial hypertension, accompanied by symptoms of adrenergic stimulation.
Collapse
|
20
|
Wu S, Longley MJ, Lujan SA, Kunkel TA, Copeland WC. Mitochondrial DNA Enrichment for Sensitive Next-Generation Sequencing. Methods Mol Biol 2023; 2615:427-441. [PMID: 36807807 DOI: 10.1007/978-1-0716-2922-2_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes components essential for cellular respiration. Low levels of point mutations and deletions accumulate in mtDNA during normal aging. However, improper maintenance of mtDNA results in mitochondrial diseases, stemming from progressive loss of mitochondrial function through the accelerated formation of deletions and mutations in mtDNA. To better understand the molecular mechanisms underlying the creation and propagation of mtDNA deletions, we developed the LostArc next-generation DNA sequencing pipeline to detect and quantify rare mtDNA species in small tissue samples. LostArc procedures are designed to minimize PCR amplification of mtDNA and instead achieve enrichment of mtDNA by selective destruction of nuclear DNA. This approach leads to cost-effective, high-depth sequencing of mtDNA with a sensitivity sufficient to identify one mtDNA deletion per million mtDNA circles. Here, we describe detailed protocols for isolation of genomic DNA from mouse tissues, enrichment of mtDNA through enzymatic destruction of linear nuclear DNA, and preparation of libraries for unbiased next-generation sequencing of mtDNA.
Collapse
Affiliation(s)
- Shilan Wu
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
| |
Collapse
|
21
|
López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. Hallmarks of aging: An expanding universe. Cell 2023; 186:243-278. [PMID: 36599349 DOI: 10.1016/j.cell.2022.11.001] [Citation(s) in RCA: 911] [Impact Index Per Article: 911.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/19/2022] [Accepted: 11/01/2022] [Indexed: 01/05/2023]
Abstract
Aging is driven by hallmarks fulfilling the following three premises: (1) their age-associated manifestation, (2) the acceleration of aging by experimentally accentuating them, and (3) the opportunity to decelerate, stop, or reverse aging by therapeutic interventions on them. We propose the following twelve hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. These hallmarks are interconnected among each other, as well as to the recently proposed hallmarks of health, which include organizational features of spatial compartmentalization, maintenance of homeostasis, and adequate responses to stress.
Collapse
Affiliation(s)
- Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Cambridge, UK
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| |
Collapse
|
22
|
López-Otín C, Pietrocola F, Roiz-Valle D, Galluzzi L, Kroemer G. Meta-hallmarks of aging and cancer. Cell Metab 2023; 35:12-35. [PMID: 36599298 DOI: 10.1016/j.cmet.2022.11.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Both aging and cancer are characterized by a series of partially overlapping "hallmarks" that we subject here to a meta-analysis. Several hallmarks of aging (i.e., genomic instability, epigenetic alterations, chronic inflammation, and dysbiosis) are very similar to specific cancer hallmarks and hence constitute common "meta-hallmarks," while other features of aging (i.e., telomere attrition and stem cell exhaustion) act likely to suppress oncogenesis and hence can be viewed as preponderantly "antagonistic hallmarks." Disabled macroautophagy and cellular senescence are two hallmarks of aging that exert context-dependent oncosuppressive and pro-tumorigenic effects. Similarly, the equivalence or antagonism between aging-associated deregulated nutrient-sensing and cancer-relevant alterations of cellular metabolism is complex. The agonistic and antagonistic relationship between the processes that drive aging and cancer has bearings for the age-related increase and oldest age-related decrease of cancer morbidity and mortality, as well as for the therapeutic management of malignant disease in the elderly.
Collapse
Affiliation(s)
- Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Federico Pietrocola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| |
Collapse
|
23
|
Holt AG, Davies AM. A comparison of mtDNA deletion mutant proliferation mechanisms. J Theor Biol 2022; 551-552:111244. [PMID: 35973607 DOI: 10.1016/j.jtbi.2022.111244] [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: 04/26/2022] [Revised: 07/17/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022]
Abstract
In this paper we use simulation methods to investigate the proliferation of deletion mutations of mitochondrial DNA in neurons. We simulate three mtDNA proliferation mechanisms, namely, random drift, replicative advantage and vicious cycle. For each mechanism, we investigated the effect mutation rates have on neuron loss within a human host. We also compare heteroplasmy of each mechanism at mutation rates that yield the levels neuron loss that would be associated with dementia. Both random drift and vicious cycle predicted high levels of heteroplasmy, while replicative advantage showed a small number of dominant clones with a low background of heteroplasmy.
Collapse
|
24
|
Leuthner T, Benzing L, Kohrn B, Bergemann C, Hipp M, Hershberger K, Mello D, Sokolskyi T, Stevenson K, Merutka I, Seay S, Gregory S, Kennedy S, Meyer J. Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans. Nucleic Acids Res 2022; 50:8626-8642. [PMID: 35947695 PMCID: PMC9410910 DOI: 10.1093/nar/gkac666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. Detection of thousands of mtDNA mutations revealed pervasive heteroplasmy in C. elegans and that mtDNA mutagenesis is dominated by C:G → A:T mutations generally attributed to oxidative damage. However, there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature despite a significant increase in nuclear mutation rate after aflatoxin B1 exposure. Mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in mtDNA mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.
Collapse
Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Laura Benzing
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Danielle F Mello
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Tymofii Sokolskyi
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Kevin Stevenson
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Ilaria R Merutka
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Sarah A Seay
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA,Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Joel N Meyer
- To whom correspondence should be addressed. Tel: +1 919 613 8109;
| |
Collapse
|
25
|
Desquiret-Dumas V, D’Ottavi M, Monnin A, Goudenège D, Méda N, Vizeneux A, Kankasa C, Tylleskar T, Bris C, Procaccio V, Nagot N, Van de Perre P, Reynier P, Molès JP. Long-Term Persistence of Mitochondrial DNA Instability in HIV-Exposed Uninfected Children during and after Exposure to Antiretroviral Drugs and HIV. Biomedicines 2022; 10:biomedicines10081786. [PMID: 35892686 PMCID: PMC9331317 DOI: 10.3390/biomedicines10081786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-exposed uninfected (HEU) children show impaired health outcomes during childhood. A high rate of mitochondrial DNA (mtDNA) instability was reported in the blood of HEU at birth. We aimed to explore the relationship between these health outcomes and mtDNA deletions over time in a case series of 24 HEU children. MtDNA instability was assessed by deep sequencing and analyzed by eKLIPse-v2 algorithm at three time points, namely birth, 1 year, and 6 years of age. Association between mtDNA deletion and health outcomes, including growth, clinical, and neurodevelopmental parameters, were explored using univariate statistical analyses and after stratification with relevant variables. HEU children were selected with an equal male:female ratio. An elevated number of mtDNA deletions and duplications events was observed at 7 days’ post-partum. Median heteroplasmy increased at one year of life and then returned to baseline by six years of age. The mtDNA instability was acquired and was not transmitted by the mother. No risk factors were significantly associated with mtDNA instability. In this small case series, we did not detect any association between any health outcome at 6 years and mtDNA instability measures. A significant effect modification of the association between the duration of maternal prophylaxis and child growth was observed after stratification with heteroplasmy rate. Genomic instability persists over time among HEU children but, despite its extension, stays subclinical at six years.
Collapse
Affiliation(s)
- Valérie Desquiret-Dumas
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Morgana D’Ottavi
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Audrey Monnin
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - David Goudenège
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Nicolas Méda
- Centre MURAZ, Bobo-Dioulasso 01 B.P. 390, Burkina Faso;
| | - Amélie Vizeneux
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Chipepo Kankasa
- Department of Paediatrics and Child Health, University Teaching Hospital, Lusaka P.O. Box 50001, Zambia;
| | - Thorkild Tylleskar
- Centre for International Health, University of Bergen, N-5020 Bergen, Norway;
| | - Céline Bris
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
| | - Pascal Reynier
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000 Angers, France; (V.D.-D.); (D.G.); (C.B.); (V.P.); (P.R.)
- UMR MITOVASC, CNRS 6015, INSERM U1083, University of Angers, F-49000 Angers, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic and Emerging Infections, INSERM, Etablissement Français du Sang, University of Montpellier, University of Antilles, F-34394 Montpellier, France; (M.D.); (A.M.); (A.V.); (N.N.); (P.V.d.P.)
- Correspondence: ; Tel.: +33-434-35-91-07
| |
Collapse
|
26
|
Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation. Mitochondrion 2022; 65:176-183. [PMID: 35787470 DOI: 10.1016/j.mito.2022.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/11/2022] [Accepted: 06/19/2022] [Indexed: 11/21/2022]
Abstract
The mitochondrial genome (mtDNA) is an important source of disease-causing genetic variability, but existing sequencing methods limit understanding, precluding phased measurement of mutations and clear detection of large sporadic deletions. We adapted a method for amplification-free sequence enrichment using Cas9 cleavage to obtain full length nanopore reads of mtDNA. We then utilized the long reads to phase mutations in a patient with an mtDNA-linked syndrome and demonstrated that this method can map age-induced mtDNA deletions. We believe this method will offer deeper insight into our understanding of mtDNA variation.
Collapse
|
27
|
Rahman MM, Young CKJ, Goffart S, Pohjoismäki JLO, Young MJ. Heterozygous p.Y955C mutation in DNA polymerase γ leads to alterations in bioenergetics, complex I subunit expression, and mtDNA replication. J Biol Chem 2022; 298:102196. [PMID: 35760101 PMCID: PMC9307957 DOI: 10.1016/j.jbc.2022.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
In human cells, ATP is generated using oxidative phosphorylation machinery, which is inoperable without proteins encoded by mitochondrial DNA (mtDNA). The DNA polymerase gamma (Polγ) repairs and replicates the multicopy mtDNA genome in concert with additional factors. The Polγ catalytic subunit is encoded by the POLG gene, and mutations in this gene cause mtDNA genome instability and disease. Barriers to studying the molecular effects of disease mutations include scarcity of patient samples and a lack of available mutant models; therefore, we developed a human SJCRH30 myoblast cell line model with the most common autosomal dominant POLG mutation, c.2864A>G/p.Y955C, as individuals with this mutation can present with progressive skeletal muscle weakness. Using on-target sequencing, we detected a 50% conversion frequency of the mutation, confirming heterozygous Y955C substitution. We found mutated cells grew slowly in a glucose-containing medium and had reduced mitochondrial bioenergetics compared with the parental cell line. Furthermore, growing Y955C cells in a galactose-containing medium to obligate mitochondrial function enhanced these bioenergetic deficits. Also, we show complex I NDUFB8 and ND3 protein levels were decreased in the mutant cell line, and the maintenance of mtDNA was severely impaired (i.e., lower copy number, fewer nucleoids, and an accumulation of Y955C-specific replication intermediates). Finally, we show the mutant cells have increased sensitivity to the mitochondrial toxicant 2′-3′-dideoxycytidine. We expect this POLG Y955C cell line to be a robust system to identify new mitochondrial toxicants and therapeutics to treat mitochondrial dysfunction.
Collapse
Affiliation(s)
- Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901.
| |
Collapse
|
28
|
Abstract
Mitochondria are the main source of energy used to maintain cellular homeostasis. This aspect of mitochondrial biology underlies their putative role in age-associated tissue dysfunction. Proper functioning of the electron transport chain (ETC), which is partially encoded by the extra-nuclear mitochondrial genome (mtDNA), is key to maintaining this energy production. The acquisition of de novo somatic mutations that interrupt the function of the ETC have long been associated with aging and common diseases of the elderly. Yet, despite over 30 years of study, the exact role(s) mtDNA mutations play in driving aging and its associated pathologies remains under considerable debate. Furthermore, even fundamental aspects of age-related mtDNA mutagenesis, such as when mutations arise during aging, where and how often they occur across tissues, and the specific mechanisms that give rise to them, remain poorly understood. In this review, we address the current understanding of the somatic mtDNA mutations, with an emphasis of when, where, and how these mutations arise during aging. Additionally, we highlight current limitations in our knowledge and critically evaluate the controversies stemming from these limitations. Lastly, we highlight new and emerging technologies that offer potential ways forward in increasing our understanding of somatic mtDNA mutagenesis in the aging process.
Collapse
Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| |
Collapse
|
29
|
Valiente-Pallejà A, Tortajada J, Bulduk BK, Vilella E, Garrabou G, Muntané G, Martorell L. Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review. EBioMedicine 2022; 76:103815. [PMID: 35085849 PMCID: PMC8790490 DOI: 10.1016/j.ebiom.2022.103815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health and disease could be a cornerstone in disentangling the relationship between biochemical findings and clinical symptoms of brain disorders. This systematic review aimed to summarize the mtDNA alterations in human brain tissue reported to date that have implications for further research on the pathophysiological significance of mtDNA alterations in brain functioning. METHODS We searched the PubMed and Embase databases using distinct terms related to postmortem human brain and mtDNA up to June 10, 2021. Reports were eligible if they were empirical studies analysing mtDNA in postmortem human brains. FINDINGS A total of 158 of 637 studies fulfilled the inclusion criteria and were clustered into the following groups: MitD (48 entries), neurological diseases (NeuD, 55 entries), psychiatric diseases (PsyD, 15 entries), a miscellaneous group with controls and other clinical diseases (5 entries), ageing (20 entries), and technical issues (5 entries). Ten entries were ascribed to more than one group. Pathogenic single nucleotide variants (pSNVs), both homo- or heteroplasmic variants, have been widely reported in MitD, with heteroplasmy levels varying among brain regions; however, pSNVs are rarer in NeuD, PsyD and ageing. A lower mtDNA copy number (CN) in disease was described in most, but not all, of the identified studies. mtDNA deletions were identified in individuals in the four clinical categories and ageing. Notably, brain samples showed significantly more mtDNA deletions and at higher heteroplasmy percentages than blood samples, and several of the deletions present in the brain were not detected in the blood. Finally, mtDNA heteroplasmy, mtDNA CN and the deletion levels varied depending on the brain region studied. INTERPRETATION mtDNA alterations are well known to affect human tissues, including the brain. In general, we found that studies of MitD, NeuD, PsyD, and ageing were highly variable in terms of the type of disease or ageing process investigated, number of screened individuals, studied brain regions and technology used. In NeuD and PsyD, no particular type of mtDNA alteration could be unequivocally assigned to any specific disease or diagnostic group. However, the presence of mtDNA deletions and mtDNA CN variation imply a role for mtDNA in NeuD and PsyD. Heteroplasmy levels and threshold effects, affected brain regions, and mitotic segregation patterns of mtDNA alterations may be involved in the complex inheritance of NeuD and PsyD and in the ageing process. Therefore, more information is needed regarding the type of mtDNA alteration, the affected brain regions, the heteroplasmy levels, and their relationship with clinical phenotypes and the ageing process. FUNDING Hospital Universitari Institut Pere Mata; Institut d'Investigació Sanitària Pere Virgili; Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (PI18/00514).
Collapse
Affiliation(s)
- Alba Valiente-Pallejà
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Juan Tortajada
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Bengisu K Bulduk
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Elisabet Vilella
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function, Department of Internal Medicine-Hospital Clínic of Barcelona (HCB); Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), 08036 Barcelona, Catalonia, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Gerard Muntané
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain; Institute of Evolutionary Biology (IBE), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain
| | - Lourdes Martorell
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain.
| |
Collapse
|
30
|
Dabravolski SA, Nikiforov NG, Zhuravlev AD, Orekhov NA, Grechko AV, Orekhov AN. Role of the mtDNA Mutations and Mitophagy in Inflammaging. Int J Mol Sci 2022; 23:ijms23031323. [PMID: 35163247 PMCID: PMC8836173 DOI: 10.3390/ijms23031323] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Ageing is an unavoidable multi-factorial process, characterised by a gradual decrease in physiological functionality and increasing vulnerability of the organism to environmental factors and pathogens, ending, eventually, in death. One of the most elaborated ageing theories implies a direct connection between ROS-mediated mtDNA damage and mutations. In this review, we focus on the role of mitochondrial metabolism, mitochondria generated ROS, mitochondrial dynamics and mitophagy in normal ageing and pathological conditions, such as inflammation. Also, a chronic form of inflammation, which could change the long-term status of the immune system in an age-dependent way, is discussed. Finally, the role of inflammaging in the most common neurodegenerative diseases, such as Alzheimer’s and Parkinson’s, is also discussed.
Collapse
Affiliation(s)
- Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], 7/11 Dovatora Str., 210026 Vitebsk, Belarus
- Correspondence:
| | - Nikita G. Nikiforov
- AP Avtsyn Research Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia; (N.G.N.); (A.D.Z.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, 119334 Moscow, Russia
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia
| | - Alexander D. Zhuravlev
- AP Avtsyn Research Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia; (N.G.N.); (A.D.Z.)
| | - Nikolay A. Orekhov
- Institute for Atherosclerosis Research, Osennyaya Street 4-1-207, 121609 Moscow, Russia; (N.A.O.); (A.N.O.)
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 14-3 Solyanka Street, 109240 Moscow, Russia;
| | - Alexander N. Orekhov
- Institute for Atherosclerosis Research, Osennyaya Street 4-1-207, 121609 Moscow, Russia; (N.A.O.); (A.N.O.)
| |
Collapse
|
31
|
Wang J, Balciuniene J, Diaz-Miranda MA, McCormick EM, Aref-Eshghi E, Muir AM, Cao K, Troiani J, Moseley A, Fan Z, Zolkipli-Cunningham Z, Goldstein A, Ganetzky RD, Muraresku CC, Peterson JT, Spinner NB, Wallace DC, Dulik MC, Falk MJ. Advanced approach for comprehensive mtDNA genome testing in mitochondrial disease. Mol Genet Metab 2022; 135:93-101. [PMID: 34969639 PMCID: PMC8877466 DOI: 10.1016/j.ymgme.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 01/16/2023]
Abstract
Mitochondrial disease diagnosis requires interrogation of both nuclear and mitochondrial (mtDNA) genomes for single-nucleotide variants (SNVs) and copy number alterations, both in the proband and often maternal relatives, together with careful phenotype correlation. We developed a comprehensive mtDNA sequencing test ('MitoGenome') using long-range PCR (LR-PCR) to amplify the full length of the mtDNA genome followed by next generation sequencing (NGS) to accurately detect SNVs and large-scale mtDNA deletions (LSMD), combined with droplet digital PCR (ddPCR) for LSMD heteroplasmy quantification. Overall, MitoGenome tests were performed on 428 samples from 394 patients with suspected or confirmed mitochondrial disease. The positive yield was 11% (43/394), including 34 patients with pathogenic or likely pathogenic SNVs (the most common being m.3243A > G in 8/34 (24%) patients), 8 patients with single LSMD, and 3 patients with multiple LSMD exceeding 10% heteroplasmy levels. Two patients with both LSMD and pathogenic SNV were detected. Overall, this LR-PCR/NGS assay provides a highly accurate and comprehensive diagnostic method for simultaneous mtDNA SNV detection at heteroplasmy levels as low as 1% and LSMD detection at heteroplasmy levels below 10%. Inclusion of maternal samples for variant classification and ddPCR to quantify LSMD heteroplasmy levels further enables accurate pathogenicity assessment and clinical correlation interpretation of mtDNA genome sequence variants and copy number alterations.
Collapse
Affiliation(s)
- Jing Wang
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maria Alejandra Diaz-Miranda
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alison M Muir
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Juliana Troiani
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alicia Moseley
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhiqian Fan
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy Goldstein
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca D Ganetzky
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colleen C Muraresku
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - James T Peterson
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
32
|
Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
Collapse
Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
33
|
Holt AG, Davies AM. The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells. Acta Biotheor 2021; 69:671-695. [PMID: 34131800 DOI: 10.1007/s10441-021-09417-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/07/2021] [Indexed: 01/21/2023]
Abstract
The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions ([Formula: see text]) have a replicative advantage over wild-type ([Formula: see text]) and that this is detrimental to the host cell, especially in post-mitotic cells. An individual cell can be viewed as forming a closed ecosystem containing a large population of independently replicating mtDNA. Within this enclosed environment a selfishly replicating [Formula: see text] would compete with the [Formula: see text] for space and resources to the detriment of the host cell. In this paper, we use a computer simulation to model cell survival in an environment where [Formula: see text] compete with [Formula: see text] such that the cell expires upon [Formula: see text] extinction. We focus on the survival time for long lived post-mitotic cells, such as neurons. We confirm previous observations that [Formula: see text] do have a replicative advantage over [Formula: see text]. As expected, cell survival times diminished with increased mutation probabilities, however, the relationship between survival time and mutation rate was non-linear, that is, a ten-fold increase in mutation probability only halved the survival time. The results of our model also showed that a modest increase in half-life had a profound affect on extending cell survival time, thereby, mitigating the replicative advantage of [Formula: see text]. Given the relevance of mitochondrial dysfunction to various neurodegenerative conditions, we propose that therapies to increase mtDNA half-life could significantly delay their onset.
Collapse
|
34
|
Leuthner TC, Meyer JN. Mitochondrial DNA Mutagenesis: Feature of and Biomarker for Environmental Exposures and Aging. Curr Environ Health Rep 2021; 8:294-308. [PMID: 34761353 PMCID: PMC8826492 DOI: 10.1007/s40572-021-00329-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Mitochondrial dysfunction is a hallmark of aging. Mitochondrial genome (mtDNA) instability contributes to mitochondrial dysfunction, and mtDNA mutagenesis may contribute to aging. However, the origin of mtDNA mutations remains somewhat controversial. The goals of this review are to introduce and review recent literature on mtDNA mutagenesis and aging, address recent animal and epidemiological evidence for the effects of chemicals on mtDNA damage and mutagenesis, propose hypotheses regarding the contribution of environmental toxicant exposure to mtDNA mutagenesis in the context of aging, and suggest future directions and approaches for environmental health researchers. RECENT FINDINGS Stressors such as pollutants, pharmaceuticals, and ultraviolet radiation can damage the mitochondrial genome or disrupt mtDNA replication, repair, and organelle homeostatic processes, potentially influencing the rate of accumulation of mtDNA mutations. Accelerated mtDNA mutagenesis could contribute to aging, diseases of aging, and sensitize individuals with pathogenic mtDNA variants to stressors. We propose three potential mechanisms of toxicant-induced effects on mtDNA mutagenesis over lifespan: (1) increased de novo mtDNA mutations, (2) altered frequencies of mtDNA mutations, or (3) both. There are remarkably few studies that have investigated the impact of environmental chemical exposures on mtDNA instability and mutagenesis, and even fewer in the context of aging. More studies are warranted because people are exposed to tens of thousands of chemicals, and are living longer. Finally, we suggest that toxicant-induced mtDNA damage and mutational signatures may be a sensitive biomarker for some exposures.
Collapse
Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA
| | - Joel N Meyer
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA.
| |
Collapse
|
35
|
Prasuhn J, Brüggemann N. Gene Therapeutic Approaches for the Treatment of Mitochondrial Dysfunction in Parkinson's Disease. Genes (Basel) 2021; 12:genes12111840. [PMID: 34828446 PMCID: PMC8623067 DOI: 10.3390/genes12111840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Mitochondrial dysfunction has been identified as a pathophysiological hallmark of disease onset and progression in patients with Parkinsonian disorders. Besides the overall emergence of gene therapies in treating these patients, this highly relevant molecular concept has not yet been defined as a target for gene therapeutic approaches. Methods: This narrative review will discuss the experimental evidence suggesting mitochondrial dysfunction as a viable treatment target in patients with monogenic and idiopathic Parkinson’s disease. In addition, we will focus on general treatment strategies and crucial challenges which need to be overcome. Results: Our current understanding of mitochondrial biology in parkinsonian disorders opens up the avenue for viable treatment strategies in Parkinsonian disorders. Insights can be obtained from primary mitochondrial diseases. However, substantial knowledge gaps and unique challenges of mitochondria-targeted gene therapies need to be addressed to provide innovative treatments in the future. Conclusions: Mitochondria-targeted gene therapies are a potential strategy to improve an important primary disease mechanism in Parkinsonian disorders. However, further studies are needed to address the unique design challenges for mitochondria-targeted gene therapies.
Collapse
Affiliation(s)
- Jannik Prasuhn
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany;
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
- Center for Brain, Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany;
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
- Center for Brain, Behavior and Metabolism, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
| |
Collapse
|
36
|
Sanchez-Contreras M, Sweetwyne MT, Kohrn BF, Tsantilas KA, Hipp MJ, Schmidt EK, Fredrickson J, Whitson JA, Campbell MD, Rabinovitch PS, Marcinek DJ, Kennedy SR. A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA. Nucleic Acids Res 2021; 49:11103-11118. [PMID: 34614167 PMCID: PMC8565317 DOI: 10.1093/nar/gkab901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational ‘hot-spots’ or ‘cold-spots’. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.
Collapse
Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth K Schmidt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Matthew D Campbell
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
37
|
Picard M. Blood mitochondrial DNA copy number: What are we counting? Mitochondrion 2021; 60:1-11. [PMID: 34157430 PMCID: PMC8464495 DOI: 10.1016/j.mito.2021.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
There is growing scientific interest to develop scalable biological measures that capture mitochondrial (dys)function. Mitochondria have their own genome, the mitochondrial DNA (mtDNA). It has been proposed that the number of mtDNA copies per cell (mtDNA copy number; mtDNAcn) reflects mitochondrial health. The common availability of stored DNA material or existing DNA sequencing data, especially from blood and other easy-to-collect samples, has made its quantification a popular approach in clinical and epidemiological studies. However, the interpretation of mtDNAcn is not univocal, and either a reduction or elevation in mtDNAcn can indicate dysfunction. The major determinants of blood-derived mtDNAcn are the heterogeneous cell type composition of leukocytes and platelet abundance, which can change with time of day, aging, and with disease. Hematopoiesis is a likely driver of blood mtDNAcn. Here we discuss the rationale and available methods to quantify mtDNAcn, the influence of blood cell type variations, and consider important gaps in knowledge that need to be resolved to maximize the scientific value around the investigation of blood mtDNAcn.
Collapse
Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA.
| |
Collapse
|
38
|
Mitochondrial DNA Instability Is Common in HIV-Exposed Uninfected Newborns. J Clin Med 2021; 10:jcm10112399. [PMID: 34071681 PMCID: PMC8197798 DOI: 10.3390/jcm10112399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 01/13/2023] Open
Abstract
Worldwide, one million HIV-exposed uninfected (HEU) children are born yearly, and chronic health impairments have been reported in these children. Mitochondrial DNA (mtDNA) instability and altered mtDNA content have been evidenced in these children, but an exhaustive characterization of altered mitochondrial genomes has never been reported. We applied deep mtDNA sequencing coupled to the deletion identification algorithm eKLIPse to the blood of HEU neonates (n = 32), which was compared with healthy controls (n = 15). Dried blood spots (DBS) from African HEU children were collected seven days after birth between November 2009 and May 2012. DBS from French healthy controls were collected at birth (or <3 days of life) in 2012 and in 2019. In contrast to the absence of mtDNA instability observed at the nucleotide level, we identified significant amounts of heteroplasmic mtDNA deletions in 75% of HEU children and in none of controls. The heteroplasmy rate of the 62 mtDNA deletions identified varied from 0.01% to up to 50%, the highest rates being broadly compatible with bioenergetic defect and clinical expression. mtDNA integrity is commonly affected in HEU neonates. The nature of the deletions suggests a mechanism related to aging or tumor-associated mtDNA instability. This child population may be at risk of additional mtDNA genetic alterations considering that they will be exposed to other mitotoxic drugs including antiretroviral or anti-tuberculosis treatment.
Collapse
|
39
|
Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
Collapse
|
40
|
Sullivan ED, Longley MJ, Copeland WC. Polymerase γ efficiently replicates through many natural template barriers but stalls at the HSP1 quadruplex. J Biol Chem 2021; 295:17802-17815. [PMID: 33454015 DOI: 10.1074/jbc.ra120.015390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Indexed: 12/27/2022] Open
Abstract
Faithful replication of the mitochondrial genome is carried out by a set of key nuclear-encoded proteins. DNA polymerase γ is a core component of the mtDNA replisome and the only replicative DNA polymerase localized to mitochondria. The asynchronous mechanism of mtDNA replication predicts that the replication machinery encounters dsDNA and unique physical barriers such as structured genes, G-quadruplexes, and other obstacles. In vitro experiments here provide evidence that the polymerase γ heterotrimer is well-adapted to efficiently synthesize DNA, despite the presence of many naturally occurring roadblocks. However, we identified a specific G-quadruplex-forming sequence at the heavy-strand promoter (HSP1) that has the potential to cause significant stalling of mtDNA replication. Furthermore, this structured region of DNA corresponds to the break site for a large (3,895 bp) deletion observed in mitochondrial disease patients. The presence of this deletion in humans correlates with UV exposure, and we have found that efficiency of polymerase γ DNA synthesis is reduced after this quadruplex is exposed to UV in vitro.
Collapse
Affiliation(s)
- Eric D Sullivan
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Matthew J Longley
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - William C Copeland
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| |
Collapse
|
41
|
Scozzi D, Cano M, Ma L, Zhou D, Zhu JH, O'Halloran JA, Goss C, Rauseo AM, Liu Z, Sahu SK, Peritore V, Rocco M, Ricci A, Amodeo R, Aimati L, Ibrahim M, Hachem R, Kreisel D, Mudd PA, Kulkarni HS, Gelman AE. Circulating mitochondrial DNA is an early indicator of severe illness and mortality from COVID-19. JCI Insight 2021; 6:143299. [PMID: 33444289 PMCID: PMC7934921 DOI: 10.1172/jci.insight.143299] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
BackgroundMitochondrial DNA (MT-DNA) are intrinsically inflammatory nucleic acids released by damaged solid organs. Whether circulating cell-free MT-DNA quantitation could be used to predict the risk of poor COVID-19 outcomes remains undetermined.MethodsWe measured circulating MT-DNA levels in prospectively collected, cell-free plasma samples from 97 subjects with COVID-19 at hospital presentation. Our primary outcome was mortality. Intensive care unit (ICU) admission, intubation, vasopressor, and renal replacement therapy requirements were secondary outcomes. Multivariate regression analysis determined whether MT-DNA levels were independent of other reported COVID-19 risk factors. Receiver operating characteristic and area under the curve assessments were used to compare MT-DNA levels with established and emerging inflammatory markers of COVID-19.ResultsCirculating MT-DNA levels were highly elevated in patients who eventually died or required ICU admission, intubation, vasopressor use, or renal replacement therapy. Multivariate regression revealed that high circulating MT-DNA was an independent risk factor for these outcomes after adjusting for age, sex, and comorbidities. We also found that circulating MT-DNA levels had a similar or superior area under the curve when compared against clinically established measures of inflammation and emerging markers currently of interest as investigational targets for COVID-19 therapy.ConclusionThese results show that high circulating MT-DNA levels are a potential early indicator for poor COVID-19 outcomes.FundingWashington University Institute of Clinical Translational Sciences COVID-19 Research Program and Washington University Institute of Clinical Translational Sciences (ICTS) NIH grant UL1TR002345.
Collapse
Affiliation(s)
- Davide Scozzi
- Division of Cardiothoracic Surgery, Department of Surgery
| | - Marlene Cano
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Lina Ma
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Dequan Zhou
- Division of Cardiothoracic Surgery, Department of Surgery
| | - Ji Hong Zhu
- Division of Cardiothoracic Surgery, Department of Surgery
| | | | - Charles Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Zhiyi Liu
- Division of Cardiothoracic Surgery, Department of Surgery
| | - Sanjaya K Sahu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Monica Rocco
- Division of Anesthesiology, Department of Medical-Surgical Science and Translational Medicine, Sapienza University of Rome, Rome, Italy
| | - Alberto Ricci
- Division of Pulmonology, Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Rachele Amodeo
- Laboratory Analysis-Flow Cytometry Section, Sapienza University of Rome, Rome, Italy
| | - Laura Aimati
- Laboratory Analysis-Flow Cytometry Section, Sapienza University of Rome, Rome, Italy
| | - Mohsen Ibrahim
- Division of Cardiothoracic Surgery, Department of Surgery.,Division of Thoracic Surgery and
| | - Ramsey Hachem
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Daniel Kreisel
- Division of Cardiothoracic Surgery, Department of Surgery
| | | | - Hrishikesh S Kulkarni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Molecular Microbiology, and
| | - Andrew E Gelman
- Division of Cardiothoracic Surgery, Department of Surgery.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
42
|
Pabis K. Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan. Mech Ageing Dev 2021; 194:111429. [PMID: 33422563 DOI: 10.1016/j.mad.2021.111429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.
Collapse
Affiliation(s)
- Kamil Pabis
- Georg August University of Göttingen, Göttingen, Germany.
| |
Collapse
|