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Comparison of mitochondrial DNA sequences from whole blood and lymphoblastoid cell lines. Sci Rep 2022; 12:1801. [PMID: 35110616 PMCID: PMC8810874 DOI: 10.1038/s41598-022-05814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/10/2022] [Indexed: 01/19/2023] Open
Abstract
Lymphoblastoid cell lines (LCLs) provide an unlimited source of genomic DNA for genetic studies. Here, we compared mtDNA sequence variants, heteroplasmic or homplasmic, between LCL (sequenced by mitoRCA-seq method) and whole blood samples (sequenced through whole genome sequencing approach) of the same 130 participants in the Framingham Heart Study. We applied harmonization of sequence coverages and consistent quality control to mtDNA sequences. We identified 866 variation sites in the 130 LCL samples and 666 sites in the 130 blood samples. More than 94% of the identified homoplasmies were present in both LCL and blood samples while more than 70% of heteroplasmic sites were uniquely present either in LCL or in blood samples. The LCL and whole blood samples carried a similar number of homoplasmic variants (p = 0.45) per sample while the LCL carried a greater number of heteroplasmic variants than whole blood per sample (p < 2.2e−16). Furthermore, the LCL samples tended to accumulate low level heteroplasmies (heteroplasmy level in 3–25%) than their paired blood samples (p = 0.001). These results suggest that cautions should be taken in the interpretation and comparison of findings when different tissues/cell types or different sequencing technologies are applied to obtain mtDNA sequences.
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2
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Duan K, Gu Q, Petralia RS, Wang YX, Panja D, Liu X, Lehmann ML, Zhu H, Zhu J, Li Z. Mitophagy in the basolateral amygdala mediates increased anxiety induced by aversive social experience. Neuron 2021; 109:3793-3809.e8. [PMID: 34614419 PMCID: PMC8639775 DOI: 10.1016/j.neuron.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/09/2021] [Accepted: 09/08/2021] [Indexed: 01/16/2023]
Abstract
Psychosocial stress is a common risk factor for anxiety disorders. The cellular mechanism for the anxiogenic effect of psychosocial stress is largely unclear. Here, we show that chronic social defeat (CSD) stress in mice causes mitochondrial impairment, which triggers the PINK1-Parkin mitophagy pathway selectively in the amygdala. This mitophagy elevation causes excessive mitochondrial elimination and consequent mitochondrial deficiency. Mitochondrial deficiency in the basolateral amygdalae (BLA) causes weakening of synaptic transmission in the BLA-BNST (bed nucleus of the stria terminalis) anxiolytic pathway and increased anxiety. The CSD-induced increase in anxiety-like behaviors is abolished in Pink1-/- and Park2-/- mice and alleviated by optogenetic activation of the BLA-BNST synapse. This study identifies an unsuspected role of mitophagy in psychogenetic-stress-induced anxiety elevation and reveals that mitochondrial deficiency is sufficient to increase anxiety and underlies the psychosocial-stress-induced anxiety increase. Mitochondria and mitophagy, therefore, can be potentially targeted to ameliorate anxiety.
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Affiliation(s)
- Kaizheng Duan
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qinhua Gu
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald S Petralia
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ya-Xian Wang
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debabrata Panja
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xing Liu
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael L Lehmann
- Section on Functional Neuroanatomy, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huiwen Zhu
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zheng Li
- Section on Synapse Development Plasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Maclaine KD, Stebbings KA, Llano DA, Havird JC. The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection. BMC Genom Data 2021; 22:52. [PMID: 34823474 PMCID: PMC8620558 DOI: 10.1186/s12863-021-01005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) codes for products necessary for electron transport and mitochondrial gene translation. mtDNA mutations can lead to human disease and influence organismal fitness. The PolG mutator mouse lacks mtDNA proofreading function and rapidly accumulates mtDNA mutations, making it a model for examining the causes and consequences of mitochondrial mutations. Premature aging in PolG mice and their physiology have been examined in depth, but the location, frequency, and diversity of their mtDNA mutations remain understudied. Identifying the locations and spectra of mtDNA mutations in PolG mice can shed light on how selection shapes mtDNA, both within and across organisms. RESULTS Here, we characterized somatic and germline mtDNA mutations in brain and liver tissue of PolG mice to quantify mutation count (number of unique mutations) and frequency (mutation prevalence). Overall, mtDNA mutation count and frequency were the lowest in the D-loop, where an mtDNA origin of replication is located, but otherwise uniform across the mitochondrial genome. Somatic mtDNA mutations have a higher mutation count than germline mutations. However, germline mutations maintain a higher frequency and were also more likely to be silent. Cytosine to thymine mutations characteristic of replication errors were the plurality of basepair changes, and missense C to T mutations primarily resulted in increased protein hydrophobicity. Unlike wild type mice, PolG mice do not appear to show strand asymmetry in mtDNA mutations. Indel mutations had a lower count and frequency than point mutations and tended to be short, frameshift deletions. CONCLUSIONS Our results provide strong evidence that purifying selection plays a major role in the mtDNA of PolG mice. Missense mutations were less likely to be passed down in the germline, and they were less likely to spread to high frequencies. The D-loop appears to have resistance to mutations, either through selection or as a by-product of replication processes. Missense mutations that decrease hydrophobicity also tend to be selected against, reflecting the membrane-bound nature of mtDNA-encoded proteins. The abundance of mutations from polymerase errors compared with reactive oxygen species (ROS) damage supports previous studies suggesting ROS plays a minimal role in exacerbating the PolG phenotype, but our findings on strand asymmetry provide discussion for the role of polymerase errors in wild type organisms. Our results provide further insight on how selection shapes mtDNA mutations and on the aging mechanisms in PolG mice.
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Affiliation(s)
- Kendra D Maclaine
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX, 78712, USA.
| | - Kevin A Stebbings
- Neuroscience Program, The University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, IL, 61801, USA
| | - Daniel A Llano
- Neuroscience Program, The University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, IL, 61801, USA
- Department of Molecular an Integrative Physiology, 524 Burrill Hall, MC-114, 407 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX, 78712, USA
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4
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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Bagge EK, Fujimori-Tonou N, Kubota-Sakashita M, Kasahara T, Kato T. Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability. BMC Biol 2020; 18:150. [PMID: 33097039 PMCID: PMC7585204 DOI: 10.1186/s12915-020-00890-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Background The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used approaches. By implementing a method to sequence mtDNA without PCR amplification prior to library preparation, we map the full unbiased mtDNA mutation spectrum across six distinct brain regions from mice. Results We demonstrate that ageing-induced levels of mtDNA mutations (single nucleotide variants and deletions) reach stable levels at 50 weeks of age but can be further elevated specifically in the cortex, nucleus accumbens (NAc), and paraventricular thalamic nucleus (PVT) by expression of a proof-reading-deficient mitochondrial DNA polymerase, PolgD181A. The increase in single nucleotide variants increases the fraction of shared SNVs as well as their frequency, while characteristics of deletions remain largely unaffected. In addition, PolgD181A also induces an ageing-dependent accumulation of non-coding control-region multimers in NAc and PVT, a feature that appears almost non-existent in wild-type mice. Conclusions Our data provide a novel view of the spatio-temporal accumulation of mtDNA mutations using very limited tissue input. The differential response of brain regions to a state of replication instability provides insight into a possible heterogenic mitochondrial landscape across the brain that may be involved in the ageing phenotype and mitochondria-associated disorders.
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Affiliation(s)
- Emilie Kristine Bagge
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Noriko Fujimori-Tonou
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mie Kubota-Sakashita
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Career Development Program, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan. .,Department of Psychiatry and Behavioral Science, Juntendo University, Graduate School of Medicine, Hongo 2-1-1, Bunkyo, Tokyo 113-8421, Japan.
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Jaberi E, Tresse E, Grønbæk K, Weischenfeldt J, Issazadeh-Navikas S. Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq). EBioMedicine 2020; 57:102868. [PMID: 32629384 PMCID: PMC7334819 DOI: 10.1016/j.ebiom.2020.102868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Point mutations and structural variations (SVs) in mitochondrial DNA (mtDNA) contribute to many neurodegenerative diseases. Technical limitations and heteroplasmy, however, have impeded their identification, preventing these changes from being examined in neurons in healthy and disease states. Methods We have developed a high-resolution technique—Mitochondrial DNA Structural Variation Sequencing (MitoSV-seq)—that identifies all types of mtDNA SVs and single-nucleotide variations (SNVs) in single neurons and novel variations that have been undetectable with conventional techniques. Findings Using MitoSV-seq, we discovered SVs/SNVs in dopaminergic neurons in the Ifnar1−/− murine model of Parkinson disease. Further, MitoSV-seq was found to have broad applicability, delivering high-quality, full-length mtDNA sequences in a species-independent manner from human PBMCs, haematological cancers, and tumour cell lines, regardless of heteroplasmy. We characterised several common SVs in haematological cancers (AML and MDS) that were linked to the same mtDNA region, MT-ND5, using only 10 cells, indicating the power of MitoSV-seq in determining single-cancer-cell ontologies. Notably, the MT-ND5 hotspot, shared between all examined cancers and Ifnar1−/− dopaminergic neurons, suggests that its mutations have clinical value as disease biomarkers. Interpretation MitoSV-seq identifies disease-relevant mtDNA mutations in single cells with high resolution, rendering it a potential drug screening platform in neurodegenerative diseases and cancers. Funding The Lundbeck Foundation, Danish Council for Independent Research-Medicine, and European Union Horizon 2020 Research and Innovation Programme.
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Affiliation(s)
- Elham Jaberi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Emilie Tresse
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kirsten Grønbæk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; Department of Hematology, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, DK-2200 Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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7
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Ishikawa K, Kobayashi K, Yamada A, Umehara M, Oka T, Nakada K. Concentration of mitochondrial DNA mutations by cytoplasmic transfer from platelets to cultured mouse cells. PLoS One 2019; 14:e0213283. [PMID: 30830936 PMCID: PMC6398856 DOI: 10.1371/journal.pone.0213283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/18/2019] [Indexed: 01/11/2023] Open
Abstract
Accumulation of mutations in mitochondrial DNA (mtDNA) is thought to be responsible for mitochondrial, and other, diseases and biological phenomena, such as diabetes, cancer, neurodegenerative diseases, and aging. Mouse models may elucidate the relationship between mutations in mtDNA and these abnormalities. However, because of the difficulty of mtDNA manipulation, generation of mouse models has not sufficiently progressed to enable such studies. To overcome this difficulty and to establish a source of diverse mtDNA mutations, we here generated cultured mouse cells containing mtDNA derived from an mtDNA mutator mouse that accumulates random mtDNA mutations with age. Mutation analysis of the obtained transmitochondrial cytoplasmic hybrid cells (cybrids) revealed that the cells harbored diverse mtDNA mutations occurring at a higher frequency than in mouse tissues, and exhibited severe respiration defects that would be lethal in tissues or organs. Abnormal respiratory complex formation and high stress on the mitochondrial protein quality control system appeared to be involved in these severe respiration defects. The mutation rates of the majority of highly accumulated mutations converged to either approximately 5%, 10%, or 40%, suggesting that these mutations are linked on the respective mtDNA molecules, and mtDNA in cybrid cells likely consisted of mtDNA molecules clonally expanded from the small population of introduced mtDNAs. Thus, the linked mutations in these cybrid cells cannot be evaluated individually. In addition, mtDNA mutations homologous to confirmed pathogenic mutations in human were rarely observed in our generated cybrids. However, the transmitochondrial cybrids constitute a useful tool for concentrating pathogenic mtDNA mutations and as a source of diverse mtDNA mutations to elucidate the relationship between mtDNA mutations and diseases.
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Affiliation(s)
- Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (KI); (KN)
| | - Kohei Kobayashi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Akihito Yamada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Moe Umehara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (KI); (KN)
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8
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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell 2019; 176:1325-1339.e22. [PMID: 30827679 DOI: 10.1016/j.cell.2019.01.022] [Citation(s) in RCA: 278] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 01/22/2023]
Abstract
Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.
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9
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Baechler SA, Factor VM, Dalla Rosa I, Ravji A, Becker D, Khiati S, Miller Jenkins LM, Lang M, Sourbier C, Michaels SA, Neckers LM, Zhang HL, Spinazzola A, Huang SN, Marquardt JU, Pommier Y. The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis. Nat Commun 2019; 10:83. [PMID: 30622257 PMCID: PMC6325124 DOI: 10.1038/s41467-018-07922-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/28/2018] [Indexed: 01/23/2023] Open
Abstract
Mitochondrial topoisomerase IB (TOP1MT) is a nuclear-encoded topoisomerase, exclusively localized to mitochondria, which resolves topological stress generated during mtDNA replication and transcription. Here, we report that TOP1MT is overexpressed in cancer tissues and demonstrate that TOP1MT deficiency attenuates tumor growth in human and mouse models of colon and liver cancer. Due to their mitochondrial dysfunction, TOP1MT-KO cells become addicted to glycolysis, which limits synthetic building blocks and energy supply required for the proliferation of cancer cells in a nutrient-deprived tumor microenvironment. Mechanistically, we show that TOP1MT associates with mitoribosomal subunits, ensuring optimal mitochondrial translation and assembly of oxidative phosphorylation complexes that are critical for sustaining tumor growth. The TOP1MT genomic signature profile, based on Top1mt-KO liver cancers, is correlated with enhanced survival of hepatocellular carcinoma patients. Our results highlight the importance of TOP1MT for tumor development, providing a potential rationale to develop TOP1MT-targeted drugs as anticancer therapies.
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MESH Headings
- Animals
- Carcinogenesis/pathology
- Carcinogens/toxicity
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Nucleus/metabolism
- Cell Proliferation
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/isolation & purification
- Datasets as Topic
- Energy Metabolism
- Female
- Fibroblasts
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Glycolysis
- HCT116 Cells
- Humans
- Liver/cytology
- Liver/metabolism
- Liver/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Liver Neoplasms, Experimental/chemically induced
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/pathology
- Male
- Mice
- Mice, Knockout
- Mice, Nude
- Mitochondria/metabolism
- Mitochondria/pathology
- Prognosis
- Protein Biosynthesis
- Survival Analysis
- Xenograft Model Antitumor Assays
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Affiliation(s)
- S A Baechler
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - V M Factor
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - I Dalla Rosa
- Department of Clinical and Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London, NW3 2PF, UK
| | - A Ravji
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - D Becker
- Department of Medicine I, Johannes Gutenberg University, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - S Khiati
- Equipe MitoLab, Institut MitoVasc, UMR CNRS 6015, INSERM U1083, Universite d'Angers, 49933, Angers, France
| | - L M Miller Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MA, 20892, USA
| | - C Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MA, 20892, USA
- Laboratory of Molecular Oncology, Division of Biotechnology Review and Research I, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - S A Michaels
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - L M Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MA, 20892, USA
| | - H L Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - A Spinazzola
- Department of Clinical and Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London, NW3 2PF, UK
| | - S N Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - J U Marquardt
- Department of Medicine I, Johannes Gutenberg University, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Y Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NIH, National Cancer Institute, Bethesda, Maryland, 20892, USA.
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10
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Samstag CL, Hoekstra JG, Huang CH, Chaisson MJ, Youle RJ, Kennedy SR, Pallanck LJ. Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ. PLoS Genet 2018; 14:e1007805. [PMID: 30452458 PMCID: PMC6289449 DOI: 10.1371/journal.pgen.1007805] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/11/2018] [Accepted: 11/01/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations cause severe maternally inherited syndromes and the accumulation of somatic mtDNA mutations is implicated in aging and common diseases. However, the mechanisms that influence the frequency and pathogenicity of mtDNA mutations are poorly understood. To address this matter, we created a Drosophila mtDNA mutator strain expressing a proofreading-deficient form of the mitochondrial DNA polymerase. Mutator flies have a dramatically increased somatic mtDNA mutation frequency that correlates with the dosage of the proofreading-deficient polymerase. Mutator flies also exhibit mitochondrial dysfunction, shortened lifespan, a progressive locomotor deficit, and loss of dopaminergic neurons. Surprisingly, the frequency of nonsynonymous, pathogenic, and conserved-site mutations in mutator flies exceeded predictions of a neutral mutational model, indicating the existence of a positive selection mechanism that favors deleterious mtDNA variants. We propose from these findings that deleterious mtDNA mutations are overrepresented because they selectively evade quality control surveillance or because they are amplified through compensatory mitochondrial biogenesis. The energy needs of an animal cell are supplied by tiny organelles known as mitochondria. Each of the many mitochondria in a cell has a set of blueprints for making more mitochondria, known as mitochondrial DNA (mtDNA). As animals age, their mtDNA acquires irreversible defects called mutations, which accumulate and may cause aging. Cells can selectively destroy malfunctioning mitochondria, so we hypothesized that mitochondria with harmful mutations would be selectively destroyed. To test our theory, we created a fruit fly strain with a high mtDNA mutation rate. Our hypothesis predicts that, because mitochondria bearing harmful mtDNA mutations would be destroyed, we should detect primarily less harmful mutations in our strain. However, the mtDNA mutations we detected were more harmful than expected by chance. We suggest two possible explanations: First, mitochondria with harmful mtDNA mutations may be degraded less often because they generate little energy and are not damaged by toxic byproducts of energy production. Second, cells may compensate for harmful mtDNA mutations by stimulating mitochondria to multiply, creating more healthy mitochondria but also more mitochondria with harmful mtDNA mutations. Future studies will distinguish between these models and further advance our understanding of aging and aging related disease.
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Affiliation(s)
- Colby L. Samstag
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Jake G. Hoekstra
- Department of Pathology, University of Washington, Seattle, WA, United States of America
| | - Chiu-Hui Huang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Mark J. Chaisson
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA, United States of America
| | - Richard J. Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, WA, United States of America
- * E-mail: (SRK); (LJP)
| | - Leo J. Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail: (SRK); (LJP)
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Faraci C, Jin J, Woods DC. Calorie restriction does not influence oocyte quality in oocytes from POLG mitochondrial mutator mice. PLoS One 2018; 13:e0204373. [PMID: 30240410 PMCID: PMC6150528 DOI: 10.1371/journal.pone.0204373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/06/2018] [Indexed: 11/26/2022] Open
Abstract
It has recently been demonstrated that moderate adult onset caloric restriction (e.g. calorie restriction; CR) has a positive impact on female fertility in aged mice, due in large to preventing the age-associated decline in the quality of oocytes available for fertilization. The impact of CR on oocyte quality has been attributed, at least in part, to mitochondrial functions. In mitochondrial DNA (mtDNA) mutator mice (PolgD257A/D257A), which harbor a mutation in the proofreading mtDNA polymerase-gamma (POLG), mitochondrial mutations rapidly accumulate, resulting in a premature aging phenotype and female infertility. As CR has been shown to extend both lifespan and ‘healthspan’ as well as improve oocyte quality in aged mice, we investigated whether adult onset CR could improve oocyte quality in the POLG mouse. Female PolgD257A/D257A mice exhibited infertility based on an inability to produce litters through natural mating. Analysis of oocytes from 8–9-month-old PolgD257A/D257A mice on CR following hormone stimulation revealed no improvement in the number of oocytes ovulated. Furthermore, CR did not result in a greater percentage of metaphase II oocytes, with the majority of the oocytes prematurely arrested at the germinal vesicle stage. Finally, CR did not improve the abnormal mitochondrial distribution or pronounced defects in meiotic spindle assembly and chromosomal distribution observed in the ad libitum fed PolgD257A/D257A. Taken together, these data suggest that although CR benefits oocyte quality and fertility outcomes in naturally aged female mice, it does not sufficiently improve oocyte quality in PolgD257A/D257A.
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Affiliation(s)
- Christine Faraci
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Joyce Jin
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Dori C. Woods
- Laboratory for Aging and Infertility Research, Department of Biology, Northeastern University, Boston, MA, United States of America
- * E-mail:
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Liu C, Fetterman JL, Liu P, Luo Y, Larson MG, Vasan RS, Zhu J, Levy D. Deep sequencing of the mitochondrial genome reveals common heteroplasmic sites in NADH dehydrogenase genes. Hum Genet 2018; 137:203-213. [PMID: 29423652 DOI: 10.1007/s00439-018-1873-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/30/2018] [Indexed: 12/17/2022]
Abstract
Increasing evidence implicates mitochondrial dysfunction in aging and age-related conditions. But little is known about the molecular basis for this connection. A possible cause may be mutations in the mitochondrial DNA (mtDNA), which are often heteroplasmic-the joint presence of different alleles at a single locus in the same individual. However, the involvement of mtDNA heteroplasmy in aging and age-related conditions has not been investigated thoroughly. We deep-sequenced the complete mtDNA genomes of 356 Framingham Heart Study participants (52% women, mean age 43, mean coverage 4570-fold), identified 2880 unique mutations and comprehensively annotated them by MITOMAP and PolyPhen-2. We discovered 11 heteroplasmic "hot" spots [NADH dehydrogenase (ND) subunit 1, 4, 5 and 6 genes, n = 7; cytochrome c oxidase I (COI), n = 2; 16S rRNA, n = 1; D-loop, n = 1] for which the alternative-to-reference allele ratios significantly increased with advancing age (Bonferroni correction p < 0.001). Four of these heteroplasmic mutations in ND and COI genes were predicted to be deleterious nonsynonymous mutations which may have direct impact on ATP production. We confirmed previous findings that healthy individuals carry many low-frequency heteroplasmy mutations with potentially deleterious effects. We hypothesize that the effect of a single deleterious heteroplasmy may be minimal due to a low mutant-to-wildtype allele ratio, whereas the aggregate effects of many deleterious mutations may cause changes in mitochondrial function and contribute to age-related diseases. The identification of age-related mtDNA mutations is an important step to understand the genetic architecture of age-related diseases and may uncover novel therapeutic targets for such diseases.
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Affiliation(s)
- Chunyu Liu
- Population Sciences Branch, NHLBI/NHI, Bethesda, MD, USA. .,Framingham Heart Study, Framingham, MA, USA. .,Department of Biostatistics, Boston University, Boston, MA, USA.
| | | | - Poching Liu
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, USA
| | - Yan Luo
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, USA
| | - Martin G Larson
- Framingham Heart Study, Framingham, MA, USA.,Department of Biostatistics, Boston University, Boston, MA, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA, USA.,School of Medicine, Boston University, Boston, MA, USA
| | - Jun Zhu
- System Biology Center, NHLBI/NHI, Bethesda, MD, USA
| | - Daniel Levy
- Population Sciences Branch, NHLBI/NHI, Bethesda, MD, USA. .,Framingham Heart Study, Framingham, MA, USA.
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13
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Ren Q, Zhang F, Xu H. Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells. Genes (Basel) 2017; 8:genes8120397. [PMID: 29257059 PMCID: PMC5748715 DOI: 10.3390/genes8120397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
In addition to chronological aging, stem cells are also subject to proliferative aging during the adult life span. However, the consequences of proliferative cycle and their contributions to stem cells aging have not been well investigated. Using Drosophila female germ line stem cells as a model, we found that the replication cycle leads to the age dependent decline of female fecundity, and is a major factor causing developmental abnormalities in the progeny of old females. The proliferative aging does not cause telomere shortening, but causes an accumulation of mitochondrial DNA (mtDNA) mutations or rearrangements at the control region. We propose that damaging mutations on mtDNA caused by accumulation of proliferation cycles in aged stem cells may disrupt mitochondrial respiration chain and impair mtDNA replication and represent a conserved mechanism underlying stem cell aging.
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Affiliation(s)
- Qiuting Ren
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Fan Zhang
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hong Xu
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Qian M, Spada C, Wang X. Approach, Application, and Bioethics of mtDNA Sequencing in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:23-38. [DOI: 10.1007/978-981-10-6674-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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