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Pabis K, Barardo D, Sirbu O, Selvarajoo K, Gruber J, Kennedy BK. A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence. eLife 2024; 12:RP87811. [PMID: 38567944 PMCID: PMC10990488 DOI: 10.7554/elife.87811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells, and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention, and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data suggest that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.
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Affiliation(s)
- Kamil Pabis
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
| | - Diogo Barardo
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
| | - Olga Sirbu
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Kumar Selvarajoo
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of SingaporeSingaporeSingapore
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Science Divisions, Yale-NUS CollegeSingaporeSingapore
| | - Brian K Kennedy
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
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Vincent AE, Chen C, Gomes TB, Di Leo V, Laalo T, Pabis K, Capaldi R, Marusich MF, McDonald D, Filby A, Fuller A, Lehmann Urban D, Zierz S, Deschauer M, Turnbull D, Reeve AK, Lawless C. A stagewise response to mitochondrial dysfunction in mitochondrial DNA maintenance disorders. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167131. [PMID: 38521420 DOI: 10.1016/j.bbadis.2024.167131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Mitochondrial DNA (mtDNA) deletions which clonally expand in skeletal muscle of patients with mtDNA maintenance disorders, impair mitochondrial oxidative phosphorylation dysfunction. Previously we have shown that these mtDNA deletions arise and accumulate in perinuclear mitochondria causing localised mitochondrial dysfunction before spreading through the muscle fibre. We believe that mito-nuclear signalling is a key contributor in the accumulation and spread of mtDNA deletions, and that knowledge of how muscle fibres respond to mitochondrial dysfunction is key to our understanding of disease mechanisms. To understand the contribution of mito-nuclear signalling to the spread of mitochondrial dysfunction, we use imaging mass cytometry. We characterise the levels of mitochondrial Oxidative Phosphorylation proteins alongside a mitochondrial mass marker, in a cohort of patients with mtDNA maintenance disorders. Our expanded panel included protein markers of key signalling pathways, allowing us to investigate cellular responses to different combinations of oxidative phosphorylation dysfunction and ragged red fibres. We find combined Complex I and IV deficiency to be most common. Interestingly, in fibres deficient for one or more complexes, the remaining complexes are often upregulated beyond the increase of mitochondrial mass typically observed in ragged red fibres. We further find that oxidative phosphorylation deficient fibres exhibit an increase in the abundance of proteins involved in proteostasis, e.g. HSP60 and LONP1, and regulation of mitochondrial metabolism (including oxidative phosphorylation and proteolysis, e.g. PHB1). Our analysis suggests that the cellular response to mitochondrial dysfunction changes depending on the combination of deficient oxidative phosphorylation complexes in each fibre.
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Affiliation(s)
- Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; John Walton Muscular Dystrophy Research Centre, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
| | - Chun Chen
- Wellcome Centre for Mitochondrial Research, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tiago Bernardino Gomes
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Valeria Di Leo
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tuomas Laalo
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kamil Pabis
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | | | - David McDonald
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Andrew Filby
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Andrew Fuller
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Stephan Zierz
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Marcus Deschauer
- Department of Neurology, Technical University Munich, Munich, Germany
| | - Doug Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
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3
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Pabis K, Chiari Y, Sala C, Straka E, Giacconi R, Provinciali M, Li X, Brown-Borg H, Nowikovsky K, Valencak TG, Gundacker C, Garagnani P, Malavolta M. Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. GeroScience 2021; 43:1975-1993. [PMID: 34117600 DOI: 10.1007/s11357-021-00393-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels.
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Affiliation(s)
- Kamil Pabis
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40126, Bologna, Italy
| | - Elisabeth Straka
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Xinna Li
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Holly Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Teresa G Valencak
- Department of Animal Science and Technology, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), and Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Bologna, Italy.,Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Kamil Pabis
- Georg August University of Göttingen, Göttingen, Germany.
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Fernandez-Mosquera L, Yambire KF, Couto R, Pereyra L, Pabis K, Ponsford AH, Diogo CV, Stagi M, Milosevic I, Raimundo N. Mitochondrial respiratory chain deficiency inhibits lysosomal hydrolysis. Autophagy 2019; 15:1572-1591. [PMID: 30917721 PMCID: PMC6693470 DOI: 10.1080/15548627.2019.1586256] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are key organelles for cellular metabolism, and regulate several processes including cell death and macroautophagy/autophagy. Here, we show that mitochondrial respiratory chain (RC) deficiency deactivates AMP-activated protein kinase (AMPK, a key regulator of energy homeostasis) signaling in tissue and in cultured cells. The deactivation of AMPK in RC-deficiency is due to increased expression of the AMPK-inhibiting protein FLCN (folliculin). AMPK is found to be necessary for basal lysosomal function, and AMPK deactivation in RC-deficiency inhibits lysosomal function by decreasing the activity of the lysosomal Ca2+ channel MCOLN1 (mucolipin 1). MCOLN1 is regulated by phosphoinositide kinase PIKFYVE and its product PtdIns(3,5)P2, which is also decreased in RC-deficiency. Notably, reactivation of AMPK, in a PIKFYVE-dependent manner, or of MCOLN1 in RC-deficient cells, restores lysosomal hydrolytic capacity. Building on these data and the literature, we propose that downregulation of the AMPK-PIKFYVE-PtdIns(3,5)P2-MCOLN1 pathway causes lysosomal Ca2+ accumulation and impaired lysosomal catabolism. Besides unveiling a novel role of AMPK in lysosomal function, this study points to the mechanism that links mitochondrial malfunction to impaired lysosomal catabolism, underscoring the importance of AMPK and the complexity of organelle cross-talk in the regulation of cellular homeostasis. Abbreviation: ΔΨm: mitochondrial transmembrane potential; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ATG5: autophagy related 5; ATP: adenosine triphosphate; ATP6V0A1: ATPase, H+ transporting, lysosomal, V0 subbunit A1; ATP6V1A: ATPase, H+ transporting, lysosomal, V0 subbunit A; BSA: bovine serum albumin; CCCP: carbonyl cyanide-m-chlorophenylhydrazone; CREB1: cAMP response element binding protein 1; CTSD: cathepsin D; CTSF: cathepsin F; DMEM: Dulbecco’s modified Eagle’s medium; DMSO: dimethyl sulfoxide; EBSS: Earl’s balanced salt solution; ER: endoplasmic reticulum; FBS: fetal bovine serum; FCCP: carbonyl cyanide-p-trifluoromethoxyphenolhydrazone; GFP: green fluorescent protein; GPN: glycyl-L-phenylalanine 2-naphthylamide; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MCOLN1/TRPML1: mucolipin 1; MEF: mouse embryonic fibroblast; MITF: melanocyte inducing transcription factor; ML1N*2-GFP: probe used to detect PtdIns(3,5)P2 based on the transmembrane domain of MCOLN1; MTORC1: mechanistic target of rapamycin kinase complex 1; NDUFS4: NADH:ubiquinone oxidoreductase subunit S4; OCR: oxygen consumption rate; PBS: phosphate-buffered saline; pcDNA: plasmid cytomegalovirus promoter DNA; PCR: polymerase chain reaction; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns(3,5)P2: phosphatidylinositol-3,5-bisphosphate; PIKFYVE: phosphoinositide kinase, FYVE-type zinc finger containing; P/S: penicillin-streptomycin; PVDF: polyvinylidene fluoride; qPCR: quantitative real time polymerase chain reaction; RFP: red fluorescent protein; RNA: ribonucleic acid; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; shRNA: short hairpin RNA; siRNA: small interfering RNA; TFEB: transcription factor EB; TFE3: transcription factor binding to IGHM enhancer 3; TMRM: tetramethylrhodamine, methyl ester, perchlorate; ULK1: unc-51 like autophagy activating kinase 1; ULK2: unc-51 like autophagy activating kinase 2; UQCRC1: ubiquinol-cytochrome c reductase core protein 1; v-ATPase: vacuolar-type H+-translocating ATPase; WT: wild-type
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Affiliation(s)
- Lorena Fernandez-Mosquera
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany.,b Doctoral Program in Molecular Medicine, Georg August University Goettingen , Goettingen , Germany
| | - King Faisal Yambire
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany.,c International Max-Planck Research School in Neuroscience , Goettingen , Germany.,d European Neuroscience Institute Goettingen, University Medical Center Goettingen and Max-Planck Society , Goettingen , Germany
| | - Renata Couto
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany.,e Doctoral Program in Molecular Biology of Cells, Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, University of Goettingen , Goettingen , Germany
| | - Leonardo Pereyra
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany.,e Doctoral Program in Molecular Biology of Cells, Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, University of Goettingen , Goettingen , Germany
| | - Kamil Pabis
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany
| | - Amy H Ponsford
- f Institute of Translational Medicine, University of Liverpool , Liverpool , UK
| | - Cátia V Diogo
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany
| | - Massimiliano Stagi
- f Institute of Translational Medicine, University of Liverpool , Liverpool , UK
| | - Ira Milosevic
- d European Neuroscience Institute Goettingen, University Medical Center Goettingen and Max-Planck Society , Goettingen , Germany
| | - Nuno Raimundo
- a Institute of Cellular Biochemistry, University Medical Center Goettingen , Goettingen , Germany
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Pabis K, Gundacker C, Giacconi R, Basso A, Costarelli L, Piacenza F, Strizzi S, Provinciali M, Malavolta M. Zinc supplementation can reduce accumulation of cadmium in aged metallothionein transgenic mice. Chemosphere 2018; 211:855-860. [PMID: 30103140 DOI: 10.1016/j.chemosphere.2018.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/19/2018] [Accepted: 08/04/2018] [Indexed: 05/13/2023]
Abstract
Epidemiologic studies suggest that exposure to Cd is related to a multitude of age-related diseases. There is evidence that Cd toxicity emerges from an interference with Zn metabolism as they compete for the same binding sites of ligands. The most responsive proteins to Cd exposure are the metal-binding proteins termed metallothioneins (MTs), which display a much greater affinity for Cd than for Zn. Most studies have considered the effect of Zn on the accumulation of exogenous Cd and tissue damage, whereas observational studies have addressed the association between Zn intake and Cd levels in body fluids. However, it has not been addressed whether supplemental Zn can lower Cd levels in organs of healthy aged animals without affecting Cu stores, a question more pertinent to human aging. We therefore aimed to investigate the effect of Zn supplementation on Cd levels in liver and kidney of aged MT transgenic mice (MT1-tg) overexpressing MT1 at levels more comparable to those observed in humans than non-transgenic mice. We found a >30% reduction of kidney and liver Cd levels in Zn supplemented MT1-tg mice compared to non-supplemented controls, independently of the dose of Zn, without a significant reduction of Cu. Our data support the idea of a causal and inverse relationship between Zn intake and Cd content in organs of aged MT1-tg mice as suggested by observational studies in humans. Our work provides the rationale for interventional studies to address the effects of Zn supplementation on Cd burden in elderly people.
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Affiliation(s)
- Kamil Pabis
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, 1090, Wien, Vienna, Austria
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, 1090, Wien, Vienna, Austria
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy
| | - Andrea Basso
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy
| | - Laura Costarelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy
| | - Sergio Strizzi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS-INRCA, Ancona, Italy.
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Vincent AE, Rosa HS, Pabis K, Lawless C, Chen C, Grünewald A, Rygiel KA, Rocha MC, Reeve AK, Falkous G, Perissi V, White K, Davey T, Petrof BJ, Sayer AA, Cooper C, Deehan D, Taylor RW, Turnbull DM, Picard M. Subcellular origin of mitochondrial DNA deletions in human skeletal muscle. Ann Neurol 2018; 84:289-301. [PMID: 30014514 PMCID: PMC6141001 DOI: 10.1002/ana.25288] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 01/07/2023]
Abstract
OBJECTIVE In patients with mitochondrial DNA (mtDNA) maintenance disorders and with aging, mtDNA deletions sporadically form and clonally expand within individual muscle fibers, causing respiratory chain deficiency. This study aimed to identify the sub-cellular origin and potential mechanisms underlying this process. METHODS Serial skeletal muscle cryosections from patients with multiple mtDNA deletions were subjected to subcellular immunofluorescent, histochemical, and genetic analysis. RESULTS We report respiratory chain-deficient perinuclear foci containing mtDNA deletions, which show local elevations of both mitochondrial mass and mtDNA copy number. These subcellular foci of respiratory chain deficiency are associated with a local increase in mitochondrial biogenesis and unfolded protein response signaling pathways. We also find that the commonly reported segmental pattern of mitochondrial deficiency is consistent with the three-dimensional organization of the human skeletal muscle mitochondrial network. INTERPRETATION We propose that mtDNA deletions first exceed the biochemical threshold causing biochemical deficiency in focal regions adjacent to the myonuclei, and induce mitochondrial biogenesis before spreading across the muscle fiber. These subcellular resolution data provide new insights into the possible origin of mitochondrial respiratory chain deficiency in mitochondrial myopathy. Ann Neurol 2018;84:289-301.
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Affiliation(s)
- Amy E Vincent
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hannah S Rosa
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kamil Pabis
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Chun Chen
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anne Grünewald
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Karolina A Rygiel
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mariana C Rocha
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Kathryn White
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Basil J Petrof
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Avan A Sayer
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals National Health Service Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Cyrus Cooper
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - David Deehan
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY.,Department of Neurology and Columbia Translational Neuroscience Initiative, H. Houston Merritt Center, Columbia University Medical Center, New York, NY.,Columbia University Aging Center, Columbia University, New York, NY
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Vincent A, Rosa H, Pabis K, Lawless C, Grünewald A, Chen C, Rygiel K, Reeve A, Rocha M, Falkous G, Perissi V, McWilliams T, Ganley I, White K, Davey T, Petrof B, Sayer A, Cooper C, Taylor R, Turnbull D, Picard M. Clonally expanded mtDNA deletions in human skeletal muscle originate as a proliferative perinuclear niche. Neuromuscul Disord 2018. [DOI: 10.1016/s0960-8966(18)30394-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Pabis K, ScheiberMojdehkar B, Valencak T, Nowikovsky K. Altered iron homeostasis in mouse models of aging. Exp Gerontol 2017. [DOI: 10.1016/j.exger.2017.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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