1
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Liufu T, Zhao X, Yu M, Xie Z, Meng L, Lv H, Zhang W, Yuan Y, Xing G, Deng J, Wang Z. Multiomics analysis reveals serine catabolism as a potential therapeutic target for MELAS. FASEB J 2024; 38:e23742. [PMID: 38865203 DOI: 10.1096/fj.202302286rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/19/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
Mitochondrial disease is a devastating genetic disorder, with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and m.3243A>G being the most common phenotype and genotype, respectively. The treatment for MELAS patients is still less effective. Here, we performed transcriptomic and proteomic analysis in muscle tissue of MELAS patients, and discovered that the expression of molecules involved in serine catabolism were significantly upregulated, and serine hydroxymethyltransferase 2 (SHMT2) increased significantly in both the mRNA and protein levels. The SHMT2 protein level was also increased in myoblasts with m.3243A>G mutation, which was transdifferentiated from patients derived fibroblasts, accompanying with the decreased nicotinamide adenine dinucleotide (NAD+)/reduced NAD+ (NADH) ratio and cell viability. After treating with SHMT2 inhibitor (SHIN1), the NAD+/NADH ratio and cell viability in MELAS myoblasts increased significantly. Taken together, our study indicates that enhanced serine catabolism plays an important role in the pathogenesis of MELAS and that SHIN1 can be a potential small molecule for the treatment of this disease.
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Affiliation(s)
- Tongling Liufu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Xutong Zhao
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
| | - Guogang Xing
- Neuroscience Research Institute, Peking University, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission, Peking University, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
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2
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Su Y, Carter JL, Li X, Fukuda Y, Gray A, Lynch J, Edwards H, Ma J, Schreiner P, Polin L, Kushner J, Dzinic SH, Buck SA, Pruett-Miller SM, Hege-Hurrish K, Robinson C, Qiao X, Liu S, Wu S, Wang G, Li J, Allen JE, Prabhu VV, Schimmer AD, Joshi D, Kalhor-Monfared S, Watson IDG, Marcellus R, Isaac MB, Al-Awar R, Taub JW, Lin H, Schuetz JD, Ge Y. The Imipridone ONC213 Targets α-Ketoglutarate Dehydrogenase to Induce Mitochondrial Stress and Suppress Oxidative Phosphorylation in Acute Myeloid Leukemia. Cancer Res 2024; 84:1084-1100. [PMID: 38266099 DOI: 10.1158/0008-5472.can-23-2659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/11/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Eradication of acute myeloid leukemia (AML) is therapeutically challenging; many patients succumb to AML despite initially responding to conventional treatments. Here, we showed that the imipridone ONC213 elicits potent antileukemia activity in a subset of AML cell lines and primary patient samples, particularly in leukemia stem cells, while producing negligible toxicity in normal hematopoietic cells. ONC213 suppressed mitochondrial respiration and elevated α-ketoglutarate by suppressing α-ketoglutarate dehydrogenase (αKGDH) activity. Deletion of OGDH, which encodes αKGDH, suppressed AML fitness and impaired oxidative phosphorylation, highlighting the key role for αKGDH inhibition in ONC213-induced death. ONC213 treatment induced a unique mitochondrial stress response and suppressed de novo protein synthesis in AML cells. Additionally, ONC213 reduced the translation of MCL1, which contributed to ONC213-induced apoptosis. Importantly, a patient-derived xenograft from a relapsed AML patient was sensitive to ONC213 in vivo. Collectively, these findings support further development of ONC213 for treating AML. SIGNIFICANCE In AML cells, ONC213 suppresses αKGDH, which induces a unique mitochondrial stress response, and reduces MCL1 to decrease oxidative phosphorylation and elicit potent antileukemia activity. See related commentary by Boët and Sarry, p. 950.
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Affiliation(s)
- Yongwei Su
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Jenna L Carter
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, Michigan
- MD/PhD Program, Wayne State University School of Medicine, Detroit, Michigan
| | - Xinyu Li
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Yu Fukuda
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ashley Gray
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee
| | - John Lynch
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Holly Edwards
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Jun Ma
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Patrick Schreiner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lisa Polin
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Juiwanna Kushner
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Sijana H Dzinic
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Steven A Buck
- Division of Pediatric Hematology/Oncology, Children's Hospital of Michigan, Detroit, Michigan
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Katie Hege-Hurrish
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, Michigan
| | - Camenzind Robinson
- St. Jude Children's Research Hospital Shared Imaging Resource, Memphis, Tennessee
| | - Xinan Qiao
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Shuang Liu
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Shuangshuang Wu
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Guan Wang
- National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, P. R. China
| | - Jing Li
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | | | | | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dhananjay Joshi
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shiva Kalhor-Monfared
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Iain D G Watson
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Methvin B Isaac
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey W Taub
- Division of Pediatric Hematology/Oncology, Children's Hospital of Michigan, Detroit, Michigan
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan
| | - Hai Lin
- Department of Hematology and Oncology, The First Hospital of Jilin University, Changchun, P.R. China
| | - John D Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yubin Ge
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
- MD/PhD Program, Wayne State University School of Medicine, Detroit, Michigan
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3
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Greenberg SA, Pinkus JL, Kong SW, Baecher-Allan C, Amato AA, Dorfman DM. Highly differentiated cytotoxic T cells in inclusion body myositis. Brain 2019; 142:2590-2604. [DOI: 10.1093/brain/awz207] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/21/2019] [Accepted: 05/16/2019] [Indexed: 01/12/2023] Open
Abstract
Abstract
Inclusion body myositis is a late onset treatment-refractory autoimmune disease of skeletal muscle associated with a blood autoantibody (anti-cN1A), an HLA autoimmune haplotype, and muscle pathology characterized by cytotoxic CD8+ T cell destruction of myofibres. Here, we report on translational studies of inclusion body myositis patient muscle compared with a diverse set of other muscle disease samples. Using available microarray data on 411 muscle samples from patients with inclusion body myositis (n = 40), other muscle diseases (n = 265), and without neuromuscular disease (normal, n = 106), we identified a signature of T-cell cytotoxicity in inclusion body myositis muscle coupled with a signature of highly differentiated CD8 T-cell effector memory and terminally differentiated effector cells. Further, we examined killer cell lectin-like receptor G1 (KLRG1) as a marker of this population of cells, demonstrated the correlation of KLRG1 gene expression with lymphocyte cytotoxicity across 28 870 human tissue samples, and identified the presence of KLRG1 on pathogenic inclusion body myositis muscle invading T cells and an increase in KLRG1 expressing T cells in inclusion body myositis blood. We examined inclusion body myositis muscle T-cell proliferation by Ki67 immunohistochemistry demonstrating that diseased muscle-invading T cells are minimally or non-proliferative, in accordance with known properties of highly differentiated or terminally differentiated T cells. We found low expression of KLRG1 on infection-protective human lymphoid tissue central memory T cells and autoimmune-protective human blood regulatory T cells. Targeting highly differentiated cytotoxic T cells could be a favourable approach to treatment of inclusion body myositis.
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Affiliation(s)
- Steven A Greenberg
- Brigham and Women’s Hospital Department of Neurology, Division of Neuromuscular Disease, and Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Jack L Pinkus
- Brigham and Women’s Hospital Department of Neurology, Division of Neuromuscular Disease, and Harvard Medical School, Boston, MA, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Clare Baecher-Allan
- Brigham and Women’s Hospital Department of Neurology, Division of Neuromuscular Disease, and Harvard Medical School, Boston, MA, USA
- Ann Romney Center for Neurologic Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Anthony A Amato
- Brigham and Women’s Hospital Department of Neurology, Division of Neuromuscular Disease, and Harvard Medical School, Boston, MA, USA
| | - David M Dorfman
- Brigham and Women’s Hospital Department of Neurology, Division of Neuromuscular Disease, and Harvard Medical School, Boston, MA, USA
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4
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Mitochondrial Transfer of Wharton's Jelly Mesenchymal Stem Cells Eliminates Mutation Burden and Rescues Mitochondrial Bioenergetics in Rotenone-Stressed MELAS Fibroblasts. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:9537504. [PMID: 31249652 PMCID: PMC6556302 DOI: 10.1155/2019/9537504] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 12/28/2022]
Abstract
Wharton's jelly mesenchymal stem cells (WJMSCs) transfer healthy mitochondria to cells harboring a mitochondrial DNA (mtDNA) defect. Mitochondrial myopathy, encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is one of the major subgroups of mitochondrial diseases, caused by the mt.3243A>G point mutation in the mitochondrial tRNALeu(UUR) gene. The specific aim of the study is to investigate whether WJMSCs exert therapeutic effect for mitochondrial dysfunction in cells of MELAS patient through donating healthy mitochondria. We herein demonstrate that WJMSCs transfer healthy mitochondria into rotenone-stressed fibroblasts of a MELAS patient, thereby eliminating mutation burden and rescuing mitochondrial functions. In the coculture system in vitro study, WJMSCs transferred healthy mitochondria to rotenone-stressed MELAS fibroblasts. By inhibiting actin polymerization to block tunneling nanotubes (TNTs), the WJMSC-conducted mitochondrial transfer was abrogated. After mitochondrial transfer, the mt.3243A>G mutation burden of MELAS fibroblasts was reduced to an undetectable level, with long-term retention. Sequencing results confirmed that the transferred mitochondria were donated from WJMSCs. Furthermore, mitochondrial transfer of WJMSCs to MELAS fibroblasts improves mitochondrial functions and cellular performance, including protein translation of respiratory complexes, ROS overexpression, mitochondrial membrane potential, mitochondrial morphology and bioenergetics, cell proliferation, mitochondrion-dependent viability, and apoptotic resistance. This study demonstrates that WJMSCs exert bioenergetic therapeutic effects through mitochondrial transfer. This finding paves the way for the development of innovative treatments for MELAS and other mitochondrial diseases.
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5
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Mayorga L, Salassa BN, Marzese DM, Loos MA, Eiroa HD, Lubieniecki F, García Samartino C, Romano PS, Roqué M. Mitochondrial stress triggers a pro-survival response through epigenetic modifications of nuclear DNA. Cell Mol Life Sci 2019; 76:1397-1417. [PMID: 30673822 PMCID: PMC11105675 DOI: 10.1007/s00018-019-03008-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/19/2018] [Accepted: 01/08/2019] [Indexed: 12/20/2022]
Abstract
Mitochondrial dysfunction represents an important cellular stressor and when intense and persistent cells must unleash an adaptive response to prevent their extinction. Furthermore, mitochondria can induce nuclear transcriptional changes and DNA methylation can modulate cellular responses to stress. We hypothesized that mitochondrial dysfunction could trigger an epigenetically mediated adaptive response through a distinct DNA methylation patterning. We studied cellular stress responses (i.e., apoptosis and autophagy) in mitochondrial dysfunction models. In addition, we explored nuclear DNA methylation in response to this stressor and its relevance in cell survival. Experiments in cultured human myoblasts revealed that intense mitochondrial dysfunction triggered a methylation-dependent pro-survival response. Assays done on mitochondrial disease patient tissues showed increased autophagy and enhanced DNA methylation of tumor suppressor genes and pathways involved in cell survival regulation. In conclusion, mitochondrial dysfunction leads to a "pro-survival" adaptive state that seems to be triggered by the differential methylation of nuclear genes.
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Affiliation(s)
- Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina.
| | - Betiana N Salassa
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Odontología, Univeridad Nacional de Cuyo- Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Diego M Marzese
- John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA, 90404, USA
| | - Mariana A Loos
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Hernán D Eiroa
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Clara García Samartino
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Patricia S Romano
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
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6
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Santacatterina F, Torresano L, Núñez-Salgado A, Esparza-Molto PB, Olive M, Gallardo E, García-Arumi E, Blazquez A, González-Quintana A, Martín MA, Cuezva JM. Different mitochondrial genetic defects exhibit the same protein signature of metabolism in skeletal muscle of PEO and MELAS patients: A role for oxidative stress. Free Radic Biol Med 2018; 126:235-248. [PMID: 30138712 DOI: 10.1016/j.freeradbiomed.2018.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Abstract
A major challenge in mitochondrial diseases (MDs) is the identification of biomarkers that could inform of the mechanisms involved in the phenotypic expression of genetic defects. Herein, we have investigated the protein signature of metabolism and of the antioxidant response in muscle biopsies of clinically and genetically diagnosed patients with Progressive External Ophthalmoplegia due to single large-scale (PEO-sD) or multiple (PEO-mD) deletions of mtDNA and Mitochondrial Encephalopathy Lactic Acidosis and Stroke-like episode (MELAS) syndrome, and healthy donors. A high-throughput immunoassay technique that quantitates the expression of relevant proteins of glycolysis, glycogenolysis, pentose phosphate pathway, oxidative phosphorylation, pyruvate and fatty acid oxidation, tricarboxylic acid cycle and the antioxidant response in two large independent and retrospectively collected cohorts of PEO-sD, PEO-mD and MELAS patients revealed that despite the heterogeneity of the genetic alterations, the three MDs showed the same metabolic signatures in both cohorts of patients, which were highly divergent from those of healthy individuals. Linear Discriminant Analysis and Support Vector Machine classifier provided a minimum of four biomarkers to discriminate healthy from pathological samples. Regardless of the induction of a large number of enzymes involved in ameliorating oxidative stress, the down-regulation of mitochondrial superoxide dismutase (SOD2) and catalase expression favored the accumulation of oxidative damage in patients' proteins. Down-regulation of SOD2 and catalase expression in MD patients is not due to relevant changes in the availability of their mRNAs, suggesting that oxidative stress regulates the expression of the two enzymes post-transcriptionally. We suggest that SOD2 and catalase could provide specific targets to improve the detoxification of reactive oxygen species that affects muscle proteins in these patients.
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Affiliation(s)
- Fulvio Santacatterina
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Laura Torresano
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Alfonso Núñez-Salgado
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain
| | - Pau B Esparza-Molto
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain
| | - Montse Olive
- Servicio de Anatomía Patológica, Unidad Patología Neuromuscular, IDIBELL-Hospital Universitario de Bellvitge, Spain
| | - Eduard Gallardo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Elena García-Arumi
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Laboratorio de Patología Mitocondrial y Neuromuscular, Área de Genética Clínica y Molecular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alberto Blazquez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - Adrián González-Quintana
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - Miguel A Martín
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain; Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario, 12 de Octubre, Madrid, Spain
| | - José M Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Spain; Instituto de Investigación Hospital, 12 de Octubre (i+12), Madrid, Spain.
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7
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Kimoloi S. Modulation of the de novo purine nucleotide pathway as a therapeutic strategy in mitochondrial myopathy. Pharmacol Res 2018; 138:37-42. [PMID: 30267763 DOI: 10.1016/j.phrs.2018.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022]
Abstract
Mitochondrial myopathy (MM) is characterised by muscle weakness, exercise intolerance and various histopathological changes. Recently, a subset of MM has also been associated with aberrant activation of mammalian target of rapamycin complex 1 (mTORC1) in skeletal muscle. This aberrant mTORC1 activation promotes increased de novo nucleotide synthesis, which contributes to abnormal expansion and imbalance of skeletal muscle deoxyribonucleoside triphosphates (dNTP) pools. However, the exact mechanism via which mTORC1-stimulated de novo nucleotide biosynthesis ultimately disturbs muscle dNTP pools remains unclear. In this article, it is proposed that mTORC1-stimulated de novo nucleotide synthesis in skeletal muscle cells with respiratory chain dysfunction promotes an asymmetric increase of purine nucleotides, probably due to NAD+ deficiency. This in turn could disrupt purine nucleotide-dependent allosteric feedback regulatory mechanisms, ultimately leading to dNTP pools aberration. Pharmacological down-modulation of aminoimidazole carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC) activity is also proposed as a potential therapeutic strategy in MM exhibiting mTORC1-driven abnormal metabolic reprogramming, including aberrant dNTPs pools.
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Affiliation(s)
- Sammy Kimoloi
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Robert Koch Street 39, Cologne, Germany; Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, P.O Box 190-50100, Kakamega, Kenya.
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8
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Lin DS, Kao SH, Ho CS, Wei YH, Hung PL, Hsu MH, Wu TY, Wang TJ, Jian YR, Lee TH, Chiang MF. Inflexibility of AMPK-mediated metabolic reprogramming in mitochondrial disease. Oncotarget 2017; 8:73627-73639. [PMID: 29088732 PMCID: PMC5650287 DOI: 10.18632/oncotarget.20617] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/17/2017] [Indexed: 01/17/2023] Open
Abstract
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is most commonly caused by the A3243G mutation of mitochondrial DNA. The capacity to utilize fatty acid or glucose as a fuel source and how such dynamic switches of metabolic fuel preferences and transcriptional modulation of adaptive mechanism in response to energy deficiency in MELAS syndrome have not been fully elucidated. The fibroblasts from patients with MELAS syndrome demonstrated a remarkable deficiency of electron transport chain complexes I and IV, an impaired cellular biogenesis under glucose deprivation, and a decreased ATP synthesis. In situ analysis of the bioenergetic properties of MELAS cells demonstrated an attenuated fatty acid oxidation that concomitantly occurred with impaired mitochondrial respiration, while energy production was mostly dependent on glycolysis. Furthermore, the transcriptional modulation was mediated by the AMP-activated protein kinase (AMPK) signaling pathway, which activated its downstream modulators leading to a subsequent increase in glycolytic flux through activation of pyruvate dehydrogenase. In contrast, the activities of carnitine palmitoyltransferase for fatty acid oxidation and acetyl-CoA carboxylase-1 for fatty acid synthesis were reduced and transcriptional regulation factors for biogenesis were not altered. These results provide novel information that MELAS cells lack the adaptive mechanism to switch fuel source from glucose to fatty acid, as glycolysis rates increase in response to energy deficiency. The aberrant secondary cellular responses to disrupted metabolic homeostasis mediated by AMPK signaling pathway may contribute to the development of the clinical phenotype.
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Affiliation(s)
- Dar-Shong Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan.,Department of Medicine, Institute of Biomedical Sciences, Mackay Medical College, New Taipei, Taiwan
| | - Shu-Huei Kao
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Che-Sheng Ho
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yau-Huei Wei
- Department of Medicine, Institute of Biomedical Sciences, Mackay Medical College, New Taipei, Taiwan.,Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua, Taiwan
| | - Pi-Lien Hung
- Department of Pediatric Neurology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Mei-Hsin Hsu
- Department of Pediatric Neurology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tsu-Yen Wu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Tuan-Jen Wang
- Department of Laboratory Medicine, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yuan-Ren Jian
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Tsung-Han Lee
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Ming-Fu Chiang
- Department of Neurosurgery, Mackay Memorial Hospital, Taipei, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Graduate Institute of Injury Prevention and Control, Taipei Medical University, Taipei, Taiwan
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9
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Wang W, Zhuang Q, Ji K, Wen B, Lin P, Zhao Y, Li W, Yan C. Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation. Sci Rep 2017; 7:41639. [PMID: 28139706 PMCID: PMC5282567 DOI: 10.1038/srep41639] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022] Open
Abstract
Researchers in the field of mitochondrial biology are increasingly unveiling of the complex mechanisms between mitochondrial dysfunction and noncoding RNAs (ncRNAs). However, roles of ncRNAs underlying mitochondrial myopathy remain unexplored. The aim of this study was to elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with mitochondrial DNA (mtDNA) A3243G mutation, which might make contributions to the unveiling of the complex mechanisms underlying mitochondrial myopathy and, possibly, new tools applicable to clinical practice. Through high-throughput technology followed by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics analyses, for the first time, we found that the dysregulated muscle miRNAs and lncRNAs between 20 MELAS patients with mtDNA A3243G mutation and 20 controls formed complex regulation networks and participated in immune system, signal transduction, translation, muscle contraction and other pathways in discovery and training phase. Then, selected ncRNAs were validated in muscle and serum in independent validation cohorts by qRT-PCR. Finally, ROC curve analysis indicated reduced serum miR-27b-3p had the better diagnosis value than lactate and might serve as a novel, noninvasive biomarker for MELAS. Follow-up investigation is warranted to better understand roles of ncRNAs in mitochondrial myopathy pathogenesis.
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Affiliation(s)
- Wei Wang
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Qianqian Zhuang
- School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Kunqian Ji
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Bing Wen
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Pengfei Lin
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Yuying Zhao
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Wei Li
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Chuanzhu Yan
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China.,Key Laboratory for Experimental Teratology of the Ministry of Education, Brain Science Research Institute, Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
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10
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Bao XR, Ong SE, Goldberger O, Peng J, Sharma R, Thompson DA, Vafai SB, Cox AG, Marutani E, Ichinose F, Goessling W, Regev A, Carr SA, Clish CB, Mootha VK. Mitochondrial dysfunction remodels one-carbon metabolism in human cells. eLife 2016; 5. [PMID: 27307216 PMCID: PMC4911214 DOI: 10.7554/elife.10575] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 05/04/2016] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial dysfunction is associated with a spectrum of human disorders, ranging from rare, inborn errors of metabolism to common, age-associated diseases such as neurodegeneration. How these lesions give rise to diverse pathology is not well understood, partly because their proximal consequences have not been well-studied in mammalian cells. Here we provide two lines of evidence that mitochondrial respiratory chain dysfunction leads to alterations in one-carbon metabolism pathways. First, using hypothesis-generating metabolic, proteomic, and transcriptional profiling, followed by confirmatory experiments, we report that mitochondrial DNA depletion leads to an ATF4-mediated increase in serine biosynthesis and transsulfuration. Second, we show that lesioning the respiratory chain impairs mitochondrial production of formate from serine, and that in some cells, respiratory chain inhibition leads to growth defects upon serine withdrawal that are rescuable with purine or formate supplementation. Our work underscores the connection between the respiratory chain and one-carbon metabolism with implications for understanding mitochondrial pathogenesis. DOI:http://dx.doi.org/10.7554/eLife.10575.001 Mitochondria are found within virtually all of our body’s cells and are best known as their power plants. Damaged mitochondria cause many diseases in humans – from rare, inherited metabolic disorders that cause symptoms including muscle weakness and developmental problems, to age-related diseases such as diabetes and Parkinson’s disease. How does mitochondrial damage lead to such a variety of symptoms and conditions? To answer this question, researchers must understand how cells respond to and compensate for such damage. To mimic mitochondrial failure, Bao et al. reduced the amount of DNA in the mitochondria of human cells and observed that this caused the cells to accumulate more of an amino acid called serine. Further investigation showed that this accumulation comes in part from cells producing more serine, and that a protein called Activating Transcription Factor 4 is responsible for increasing the expression of the genes needed to produce serine in the cells. Bao et al. also found that damaged mitochondria are less able to consume serine to produce a compound called formate, which is a precursor for DNA building blocks. If cells cannot acquire enough extra serine to compensate for this inefficiency, they cannot produce some of the building blocks required to make DNA and other critical compounds in the cell. Supplementing the cells with formate or the DNA building blocks enabled the cells to recover, which suggests that formate supplements may help to treat some mitochondrial disorders. At a higher level, these results suggest that the mitochondrion’s role as a major chemical factory in the cell, and not just as the power plant, may also contribute to disease when the mitochondria are broken. Further work is now needed to investigate how cells know to turn on Activating Transcription Factor 4 when their mitochondria are damaged. It also remains to be discovered whether this reduces or exacerbates the symptoms of mitochondrial disease. DOI:http://dx.doi.org/10.7554/eLife.10575.002
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Affiliation(s)
- Xiaoyan Robert Bao
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Shao-En Ong
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Olga Goldberger
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States
| | - Jun Peng
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Rohit Sharma
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States
| | - Dawn A Thompson
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Scott B Vafai
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Andrew G Cox
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Eizo Marutani
- Department of Anesthesia, Critical Care, and Pain Medicine, Masaschusetts General Hospital, Boston, United States
| | - Fumito Ichinose
- Department of Anesthesia, Critical Care, and Pain Medicine, Masaschusetts General Hospital, Boston, United States
| | - Wolfram Goessling
- Broad Institute of MIT and Harvard, Cambridge, United States.,Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Vamsi K Mootha
- Department of Molecular Biology, Howard Hughes Medical Institute , Massachusetts General Hospital, Boston, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
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11
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Shigi N. Sulfur Modifications in tRNA: Function and Implications for Human Disease. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Choi SB, Park JS, Chung JW, Yoo TK, Kim DW. Multicategory classification of 11 neuromuscular diseases based on microarray data using support vector machine. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:3460-3. [PMID: 25570735 DOI: 10.1109/embc.2014.6944367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We applied multicategory machine learning methods to classify 11 neuromuscular disease groups and one control group based on microarray data. To develop multicategory classification models with optimal parameters and features, we performed a systematic evaluation of three machine learning algorithms and four feature selection methods using three-fold cross validation and a grid search. This study included 114 subjects of 11 neuromuscular diseases and 31 subjects of a control group using microarray data with 22,283 probe sets from the National Center for Biotechnology Information (NCBI). We obtained an accuracy of 100%, relative classifier information (RCI) of 1.0, and a kappa index of 1.0 by applying the models of support vector machines one-versus-one (SVM-OVO), SVM one-versus-rest (OVR), and directed acyclic graph SVM (DAGSVM), using the ratio of genes between categories to within-category sums of squares (BW) feature selection method. Each of these three models selected only four features to categorize the 12 groups, resulting in a time-saving and cost-effective strategy for diagnosing neuromuscular diseases. In addition, a gene symbol, SPP1 was selected as the top-ranked gene by the BW method. We confirmed relationships between the gene (SPP1) and Duchenne muscular dystrophy (DMD) from a previous study. With our models as clinically helpful tools, neuromuscular diseases could be classified quickly using a computer, thereby giving a time-saving, cost-effective, and accurate diagnosis.
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13
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Garrido-Maraver J, Paz MV, Cordero MD, Bautista-Lorite J, Oropesa-Ávila M, de la Mata M, Pavón AD, de Lavera I, Alcocer-Gómez E, Galán F, Ybot González P, Cotán D, Jackson S, Sánchez-Alcázar JA. Critical role of AMP-activated protein kinase in the balance between mitophagy and mitochondrial biogenesis in MELAS disease. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2535-53. [PMID: 26341273 DOI: 10.1016/j.bbadis.2015.08.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Juan Garrido-Maraver
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Marina Villanueva Paz
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Mario D Cordero
- Facultad de Odontología, Universidad de Sevilla, Sevilla, Spain
| | | | - Manuel Oropesa-Ávila
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Mario de la Mata
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Ana Delgado Pavón
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Isabel de Lavera
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Elizabet Alcocer-Gómez
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | | | - Patricia Ybot González
- Instituto de Biomedicina de Sevilla (IBIS)-CSIC, Hospital Virgen del Rocío, Sevilla, Spain
| | - David Cotán
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
| | - Sandra Jackson
- Department of Neurology, Uniklinikum C. G. Carus, Dresden, Germany
| | - José A Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain.
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14
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Wei FY, Zhou B, Suzuki T, Miyata K, Ujihara Y, Horiguchi H, Takahashi N, Xie P, Michiue H, Fujimura A, Kaitsuka T, Matsui H, Koga Y, Mohri S, Suzuki T, Oike Y, Tomizawa K. Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans. Cell Metab 2015; 21:428-42. [PMID: 25738458 DOI: 10.1016/j.cmet.2015.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/24/2014] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Transfer RNAs (tRNAs) contain a wide variety of posttranscriptional modifications that are important for accurate decoding. Mammalian mitochondrial tRNAs (mt-tRNAs) are modified by nuclear-encoded tRNA-modifying enzymes; however, the physiological roles of these modifications remain largely unknown. In this study, we report that Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1) is responsible for 2-methylthio (ms(2)) modifications of mammalian mt-tRNAs for Ser(UCN), Phe, Tyr, and Trp codons. Deficiency in ms(2) modification markedly impaired mitochondrial protein synthesis, which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice. The KO mice were highly susceptive to stress-induced mitochondrial remodeling and exhibited accelerated myopathy and cardiac dysfunction under stressed conditions. Furthermore, we demonstrate that the ms(2) modifications of mt-tRNAs were sensitive to oxidative stress and were reduced in patients with mitochondrial disease. These findings highlight the fundamental role of ms(2) modifications of mt-tRNAs in mitochondrial protein synthesis and their pathological consequences in mitochondrial disease.
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Affiliation(s)
- Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Bo Zhou
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshihiro Ujihara
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Haruki Horiguchi
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Nozomu Takahashi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Peiyu Xie
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyuki Michiue
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Atsushi Fujimura
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hideki Matsui
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yasutoshi Koga
- Department of Pediatrics and Child Health, Kurume University Graduate School of Medicine, Fukuoka 830-0011, Japan
| | - Satoshi Mohri
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
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15
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Fujita Y, Ito M, Kojima T, Yatsuga S, Koga Y, Tanaka M. GDF15 is a novel biomarker to evaluate efficacy of pyruvate therapy for mitochondrial diseases. Mitochondrion 2015; 20:34-42. [DOI: 10.1016/j.mito.2014.10.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 09/02/2014] [Accepted: 10/29/2014] [Indexed: 01/15/2023]
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16
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Lindholm ME, Huss M, Solnestam BW, Kjellqvist S, Lundeberg J, Sundberg CJ. The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing. FASEB J 2014; 28:4571-81. [PMID: 25016029 DOI: 10.1096/fj.14-255000] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human skeletal muscle health is important for quality of life and several chronic diseases, including type II diabetes, heart disease, and cancer. Skeletal muscle is a tissue widely used to study mechanisms behind different diseases and adaptive effects of controlled interventions. For such mechanistic studies, knowledge about the gene expression profiles in different states is essential. Since the baseline transcriptome has not been analyzed systematically, the purpose of this study was to provide a deep reference profile of female and male skeletal muscle. RNA sequencing data were analyzed from a large set of 45 resting human muscle biopsies. We provide extensive information on the skeletal muscle transcriptome, including 5 previously unannotated protein-coding transcripts. Global transcriptional tissue homogeneity was strikingly high, within both a specific muscle and the contralateral leg. We identified >23,000 known isoforms and found >5000 isoforms that differ between the sexes. The female and male transcriptome was enriched for genes associated with oxidative metabolism and protein catabolic processes, respectively. The data demonstrate remarkably high tissue homogeneity and provide a deep and extensive baseline reference for the human skeletal muscle transcriptome, with regard to alternative splicing, novel transcripts, and sex differences in functional ontology.transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
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Affiliation(s)
- Malene E Lindholm
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden;
| | - Mikael Huss
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; and
| | - Beata W Solnestam
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Sanela Kjellqvist
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; and
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Carl J Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
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17
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Integrative analysis of independent transcriptome data for rare diseases. Methods 2014; 69:315-25. [PMID: 24981076 DOI: 10.1016/j.ymeth.2014.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 01/12/2023] Open
Abstract
High-throughput technologies used to interrogate transcriptomes have been generating a great amount of publicly available gene expression data. For rare diseases that lack of clinical samples and research funding, there is a practical benefit to jointly analyze existing data sets commonly related to a specific rare disease. In this study, we collected a number of independently generated transcriptome data sets from four species: human, fly, mouse and worm. All data sets included samples with both normal and abnormal mitochondrial function. We reprocessed each data set to standardize format, scale and gene annotation and used HomoloGene database to map genes between species. Standardized procedure was also applied to compare gene expression profiles of normal and abnormal mitochondrial function to identify differentially expressed genes. We further used meta-analysis and other integrative analyses to recognize patterns across data sets and species. Novel insights related to mitochondrial dysfunction was revealed via these analyses, such as a group of genes consistently dysregulated by impaired mitochondrial function in multiple species. This study created a template for the study of rare diseases using genomic technologies and advanced statistical methods. All data and results generated by this study are freely available and stored at http://goo.gl/nOGWC2, to support further data mining.
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18
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Zhang Z, Falk MJ. Integrated transcriptome analysis across mitochondrial disease etiologies and tissues improves understanding of common cellular adaptations to respiratory chain dysfunction. Int J Biochem Cell Biol 2014; 50:106-11. [PMID: 24569120 DOI: 10.1016/j.biocel.2014.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/10/2014] [Accepted: 02/16/2014] [Indexed: 11/25/2022]
Abstract
Mitochondrial diseases are heterogeneous, multi-systemic disorders for which mechanistic understanding is limited. To investigate common downstream effects of primary respiratory chain dysfunction on global gene expression and pathway regulation, we reanalyzed transcriptome datasets from all publicly available studies of respiratory chain dysfunction resulting from genetic disorders, acute pathophysiologic processes, or environmental toxins. A general overview is provided of the bioinformatic processing of transcriptome data to uncover biological insights into in vivo and in vitro adaptations to mitochondrial dysfunction, with specific examples discussed from a variety of independent cell, animal, and human tissue studies. To facilitate future community efforts to cohesively mine these data, all reanalyzed transcriptome datasets were deposited into a publicly accessible central web archive. Our own integrated meta-analysis of these data identified several commonly dysregulated genes across diverse mitochondrial disease etiologies, models, and tissue types. Overall, transcriptome analyses provide a useful means to survey cellular adaptation to mitochondrial diseases.
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Affiliation(s)
- Zhe Zhang
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Marni J Falk
- Division of Human Genetics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States.
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19
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Kalko SG, Paco S, Jou C, Rodríguez MA, Meznaric M, Rogac M, Jekovec-Vrhovsek M, Sciacco M, Moggio M, Fagiolari G, De Paepe B, De Meirleir L, Ferrer I, Roig-Quilis M, Munell F, Montoya J, López-Gallardo E, Ruiz-Pesini E, Artuch R, Montero R, Torner F, Nascimento A, Ortez C, Colomer J, Jimenez-Mallebrera C. Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies. BMC Genomics 2014; 15:91. [PMID: 24484525 PMCID: PMC3937154 DOI: 10.1186/1471-2164-15-91] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 01/28/2014] [Indexed: 02/08/2023] Open
Abstract
Background Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays. Results We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression. Conclusion Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Neurology Department, Fundación Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.
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20
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Zhang Z, Tsukikawa M, Peng M, Polyak E, Nakamaru-Ogiso E, Ostrovsky J, McCormack S, Place E, Clarke C, Reiner G, McCormick E, Rappaport E, Haas R, Baur JA, Falk MJ. Primary respiratory chain disease causes tissue-specific dysregulation of the global transcriptome and nutrient-sensing signaling network. PLoS One 2013; 8:e69282. [PMID: 23894440 PMCID: PMC3722174 DOI: 10.1371/journal.pone.0069282] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Primary mitochondrial respiratory chain (RC) diseases are heterogeneous in etiology and manifestations but collectively impair cellular energy metabolism. Mechanism(s) by which RC dysfunction causes global cellular sequelae are poorly understood. To identify a common cellular response to RC disease, integrated gene, pathway, and systems biology analyses were performed in human primary RC disease skeletal muscle and fibroblast transcriptomes. Significant changes were evident in muscle across diverse RC complex and genetic etiologies that were consistent with prior reports in other primary RC disease models and involved dysregulation of genes involved in RNA processing, protein translation, transport, and degradation, and muscle structure. Global transcriptional and post-transcriptional dysregulation was also found to occur in a highly tissue-specific fashion. In particular, RC disease muscle had decreased transcription of cytosolic ribosomal proteins suggestive of reduced anabolic processes, increased transcription of mitochondrial ribosomal proteins, shorter 5′-UTRs that likely improve translational efficiency, and stabilization of 3′-UTRs containing AU-rich elements. RC disease fibroblasts showed a strikingly similar pattern of global transcriptome dysregulation in a reverse direction. In parallel with these transcriptional effects, RC disease dysregulated the integrated nutrient-sensing signaling network involving FOXO, PPAR, sirtuins, AMPK, and mTORC1, which collectively sense nutrient availability and regulate cellular growth. Altered activities of central nodes in the nutrient-sensing signaling network were validated by phosphokinase immunoblot analysis in RC inhibited cells. Remarkably, treating RC mutant fibroblasts with nicotinic acid to enhance sirtuin and PPAR activity also normalized mTORC1 and AMPK signaling, restored NADH/NAD+ redox balance, and improved cellular respiratory capacity. These data specifically highlight a common pathogenesis extending across different molecular and biochemical etiologies of individual RC disorders that involves global transcriptome modifications. We further identify the integrated nutrient-sensing signaling network as a common cellular response that mediates, and may be amenable to targeted therapies for, tissue-specific sequelae of primary mitochondrial RC disease.
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Affiliation(s)
- Zhe Zhang
- Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Mai Tsukikawa
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Min Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erzsebet Polyak
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eiko Nakamaru-Ogiso
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julian Ostrovsky
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shana McCormack
- Division of Endocrinology, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Place
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Colleen Clarke
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Child Development and Metabolic Disease, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gail Reiner
- Department of Pediatrics, University of California San Diego, San Diego, California, United States of America
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Child Development and Metabolic Disease, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Rappaport
- Nucleic Acid and Protein Core Facility, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard Haas
- Department of Pediatrics, University of California San Diego, San Diego, California, United States of America
| | - Joseph A. Baur
- Department of Physiology, and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marni J. Falk
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Child Development and Metabolic Disease, The Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Garrido-Maraver J, Cordero MD, Moñino ID, Pereira-Arenas S, Lechuga-Vieco AV, Cotán D, De la Mata M, Oropesa-Ávila M, De Miguel M, Bautista Lorite J, Rivas Infante E, Alvarez-Dolado M, Navas P, Jackson S, Francisci S, Sánchez-Alcázar JA. Screening of effective pharmacological treatments for MELAS syndrome using yeasts, fibroblasts and cybrid models of the disease. Br J Pharmacol 2013; 167:1311-28. [PMID: 22747838 DOI: 10.1111/j.1476-5381.2012.02086.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE MELAS (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) is a mitochondrial disease most usually caused by point mutations in tRNA genes encoded by mitochondrial DNA (mtDNA). Approximately 80% of cases of MELAS syndrome are associated with a m.3243A > G mutation in the MT-TL1 gene, which encodes the mitochondrial tRNALeu (UUR). Currently, no effective treatments are available for this chronic progressive disorder. Treatment strategies in MELAS and other mitochondrial diseases consist of several drugs that diminish the deleterious effects of the abnormal respiratory chain function, reduce the presence of toxic agents or correct deficiencies in essential cofactors. EXPERIMENTAL APPROACH We evaluated the effectiveness of some common pharmacological agents that have been utilized in the treatment of MELAS, in yeast, fibroblast and cybrid models of the disease. The yeast model harbouring the A14G mutation in the mitochondrial tRNALeu(UUR) gene, which is equivalent to the A3243G mutation in humans, was used in the initial screening. Next, the most effective drugs that were able to rescue the respiratory deficiency in MELAS yeast mutants were tested in fibroblasts and cybrid models of MELAS disease. KEY RESULTS According to our results, supplementation with riboflavin or coenzyme Q(10) effectively reversed the respiratory defect in MELAS yeast and improved the pathologic alterations in MELAS fibroblast and cybrid cell models. CONCLUSIONS AND IMPLICATIONS Our results indicate that cell models have great potential for screening and validating the effects of novel drug candidates for MELAS treatment and presumably also for other diseases with mitochondrial impairment.
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Affiliation(s)
- Juan Garrido-Maraver
- Centro Andaluz de Biología del Desarrollo (CABD) and Centro de Investigación Biomédica en Red: Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
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Herbst A, Johnson CJ, Hynes K, McKenzie D, Aiken JM. Mitochondrial biogenesis drives a vicious cycle of metabolic insufficiency and mitochondrial DNA deletion mutation accumulation in aged rat skeletal muscle fibers. PLoS One 2013; 8:e59006. [PMID: 23516592 PMCID: PMC3596334 DOI: 10.1371/journal.pone.0059006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/08/2013] [Indexed: 01/07/2023] Open
Abstract
Aged muscles possess dysfunctional fibers that contain intracellular expansions of somatically derived mitochondrial DNA deletion mutations. At high abundance, these mutations disrupt the expression of mitochondrially-encoded protein subunits of the electron transport chain resulting in aerobic respiration deficient muscle fiber segments. These fiber segments atrophy and break contributing to the loss of muscle mass and function that occurs with age. By combining micro-dissection of individual muscle fibers with microarray analysis, we observed the response induced within these abnormal muscle fibers and detected an increase in many genes affecting metabolism and metabolic regulation. The transcriptional profile and subsequent protein validation suggested that a non-compensatory program of mitochondrial biogenesis was initiated. We hypothesized that this non-adaptive program of mitochondrial biogenesis was driving mtDNA deletion mutation accumulation. We tested this hypothesis by treating aged rats with β-Guanidinopropionic acid, a compound that stimulates mitochondrial biogenesis. β-Guanidinopropionic acid treatment increased muscle mitochondrial genome copy number and resulted in a 3.7 fold increase in the abundance of electron transport chain negative muscle fiber segments. We conclude that in electron transport system abnormal muscle fiber segments, a vicious cycle of metabolic insufficiency and non-compensatory mitochondrial biogenesis drive mtDNA deletion mutation accumulation.
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Affiliation(s)
- Allen Herbst
- Centre for Prions and Protein Folding Diseases, Agriculture Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Chad J. Johnson
- Department of Soil Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kayla Hynes
- Centre for Prions and Protein Folding Diseases, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Debbie McKenzie
- Centre for Prions and Protein Folding Diseases, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Judd M. Aiken
- Centre for Prions and Protein Folding Diseases, Agriculture Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
- * E-mail:
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23
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Haynes CM, Fiorese CJ, Lin YF. Evaluating and responding to mitochondrial dysfunction: the mitochondrial unfolded-protein response and beyond. Trends Cell Biol 2013; 23:311-8. [PMID: 23489877 DOI: 10.1016/j.tcb.2013.02.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/27/2013] [Accepted: 02/11/2013] [Indexed: 12/21/2022]
Abstract
During development and cellular differentiation, tissue- and cell-specific programs mediate mitochondrial biogenesis to meet physiological needs. However, environmental and disease-associated factors can perturb mitochondrial activities, requiring cells to adapt to protect mitochondria and maintain cellular homeostasis. Several mitochondrion-to-nucleus signaling pathways, or retrograde responses, have been described, but the mechanisms by which mitochondrial stress or dysfunction is sensed to coordinate precisely the appropriate response has only recently begun to be understood. Recent studies of the mitochondrial unfolded-protein response (UPRmt) indicate that the cell monitors mitochondrial protein import efficiency as an indicator of mitochondrial function. Here, we review how the cell evaluates mitochondrial function and regulates transcriptional induction of the UPRmt, adapts protein-synthesis rates and activates mitochondrial autophagy to promote mitochondrial function and cell survival during stress.
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Affiliation(s)
- Cole M Haynes
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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Chae S, Ahn BY, Byun K, Cho YM, Yu MH, Lee B, Hwang D, Park KS. A Systems Approach for Decoding Mitochondrial Retrograde Signaling Pathways. Sci Signal 2013; 6:rs4. [DOI: 10.1126/scisignal.2003266] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Elstner M, Turnbull DM. Transcriptome analysis in mitochondrial disorders. Brain Res Bull 2012; 88:285-93. [DOI: 10.1016/j.brainresbull.2011.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 07/24/2011] [Indexed: 12/21/2022]
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26
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Tang W, Chowdhury AR, Guha M, Huang L, Van Winkle T, Rustgi AK, Avadhani NG. Silencing of IkBβ mRNA causes disruption of mitochondrial retrograde signaling and suppression of tumor growth in vivo. Carcinogenesis 2012; 33:1762-8. [PMID: 22637744 DOI: 10.1093/carcin/bgs190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A number of studies show that mitochondrial DNA (mtDNA) depletion and attendant activation of retrograde signaling induces tumor progression. We have reported previously that activation of a novel nuclear factor-Kappa B pathway is critical for the propagation of mitochondrial retrograde signaling, which induces both phenotypic and morphological changes in C2C12 myoblasts and A549 lung carcinoma cells. In this study, we investigated the role of stress-induced nuclear factor-Kappa B in tumor progression in xenotransplanted mice. We used a retroviral system for the inducible expression of small interfering RNA against IkBα and IkBβ mRNAs. Expression of small interfering RNA against IkBβ markedly impaired tumor growth and invasive ability of mtDNA-depleted C2C12 myoblasts and also thwarted anchorage-independent growth of the cells. Knockdown of IkBα mRNA, however, did not have any modulatory effect in this cell system. Moreover, expression of small interfering RNA against IkBβ reduced the expression of marker genes for retrograde signaling and tumor growth in xenografts of mtDNA-depleted cells. Our findings demonstrate that IkBβ is a master regulator of mitochondrial retrograde signaling pathway and that the retrograde signaling plays a role in tumor growth in vivo. In this regard, IkBβ supports the tumorigenic potential of mtDNA-depleted C2C12 cells.
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Affiliation(s)
- Weigang Tang
- Department of Animal Biology and Marie Lowe Center for Comparative Oncology, University of Pennsylvania, Philadelphia, PA 19104,USA
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27
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Mende S, Royer L, Herr A, Schmiedel J, Deschauer M, Klopstock T, Kostic VS, Schroeder M, Reichmann H, Storch A. Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators. Neurol Res 2012; 33:638-55. [PMID: 21708074 DOI: 10.1179/1743132810y.0000000016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND The heteroplasmic mitochondrial DNA (mtDNA) mutation A3243G causes the mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome as one of the most frequent mitochondrial diseases. The process of reconfiguration of nuclear gene expression profile to accommodate cellular processes to the functional status of mitochondria might be a key to MELAS disease manifestation and could contribute to its diverse phenotypic presentation. OBJECTIVE To determine master regulatory protein networks and disease-modifying genes in MELAS syndrome. METHODS Analyses of whole blood transcriptomes from 10 MELAS patients using a novel strategy by combining classic Affymetrix oligonucleotide microarray profiling with regulatory and protein interaction network analyses. RESULTS Hierarchical cluster analysis elucidated that the relative abundance of mutant mtDNA molecules is decisive for the nuclear gene expression response. Further analyses confirmed not only transcription factors already known to be involved in mitochondrial diseases (such as TFAM), but also detected the hypoxia-inducible factor 1 complex, nuclear factor Y and cAMP responsive element-binding protein-related transcription factors as novel master regulators for reconfiguration of nuclear gene expression in response to the MELAS mutation. Correlation analyses of gene alterations and clinico-genetic data detected significant correlations between A3243G-induced nuclear gene expression changes and mutant mtDNA load as well as disease characteristics. These potential disease-modifying genes influencing the expression of the MELAS phenotype are mainly related to clusters primarily unrelated to cellular energy metabolism, but important for nucleic acid and protein metabolism, and signal transduction. DISCUSSION Our data thus provide a framework to search for new pathogenetic concepts and potential therapeutic approaches to treat the MELAS syndrome.
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Affiliation(s)
- Susanne Mende
- Department of Neurology, Dresden University of Technology, Germany
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28
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Jones AWE, Yao Z, Vicencio JM, Karkucinska-Wieckowska A, Szabadkai G. PGC-1 family coactivators and cell fate: roles in cancer, neurodegeneration, cardiovascular disease and retrograde mitochondria-nucleus signalling. Mitochondrion 2011; 12:86-99. [PMID: 21983689 DOI: 10.1016/j.mito.2011.09.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 09/08/2011] [Accepted: 09/16/2011] [Indexed: 12/29/2022]
Abstract
Over the past two decades, a complex nuclear transcriptional machinery controlling mitochondrial biogenesis and function has been described. Central to this network are the PGC-1 family coactivators, characterised as master regulators of mitochondrial biogenesis. Recent literature has identified a broader role for PGC-1 coactivators in both cell death and cellular adaptation under conditions of stress, here reviewed in the context of the pathology associated with cancer, neurodegeneration and cardiovascular disease. Moreover, we propose that these studies also imply a novel conceptual framework on the general role of mitochondrial dysfunction in disease. It is now well established that the complex nuclear transcriptional control of mitochondrial biogenesis allows for adaptation of mitochondrial mass and function to environmental conditions. On the other hand, it has also been suggested that mitochondria alter their function according to prevailing cellular energetic requirements and thus function as sensors that generate signals to adjust fundamental cellular processes through a retrograde mitochondria-nucleus signalling pathway. Therefore, altered mitochondrial function can affect cell fate not only directly by modifying cellular energy levels or redox state, but also indirectly, by altering nuclear transcriptional patterns. The current literature on such retrograde signalling in both yeast and mammalian cells is thus reviewed, with an outlook on its potential contribution to disease through the regulation of PGC-1 family coactivators. We propose that further investigation of these pathways will lead to the identification of novel pharmacological targets and treatment strategies to combat disease.
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Affiliation(s)
- Aleck W E Jones
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
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29
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Cotán D, Cordero MD, Garrido-Maraver J, Oropesa-Ávila M, Rodríguez-Hernández A, Gómez Izquierdo L, De la Mata M, De Miguel M, Lorite JB, Infante ER, Jackson S, Navas P, Sánchez-Alcázar JA. Secondary coenzyme Q10 deficiency triggers mitochondria degradation by mitophagy in MELAS fibroblasts. FASEB J 2011; 25:2669-87. [PMID: 21551238 DOI: 10.1096/fj.10-165340] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is a mitochondrial disease most usually caused by point mutations in tRNA genes encoded by mtDNA. Here, we report on how this mutation affects mitochondrial function in primary fibroblast cultures established from 2 patients with MELAS who harbored the A3243G mutation. Both mitochondrial respiratory chain enzyme activities and coenzyme Q(10) (CoQ) levels were significantly decreased in MELAS fibroblasts. A similar decrease in mitochondrial membrane potential was found in intact MELAS fibroblasts. Mitochondrial dysfunction was associated with increased oxidative stress and the activation of mitochondrial permeability transition (MPT), which triggered the degradation of impaired mitochondria. Furthermore, we found defective autophagosome elimination in MELAS fibroblasts. Electron and fluorescence microscopy studies confirmed a massive degradation of mitochondria and accumulation of autophagosomes, suggesting mitophagy activation and deficient autophagic flux. Transmitochondrial cybrids harboring the A3243G mutation also showed CoQ deficiency and increased autophagy activity. All these abnormalities were partially restored by CoQ supplementation. Autophagy in MELAS fibroblasts was also abolished by treatment with antioxidants or cyclosporine, suggesting that both reactive oxygen species and MPT participate in this process. Furthermore, prevention of autophagy in MELAS fibroblasts resulted in apoptotic cell death, suggesting a protective role of autophagy in MELAS fibroblasts.
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Affiliation(s)
- David Cotán
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Sevilla 41013, Spain
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Guha M, Fang JK, Monks R, Birnbaum MJ, Avadhani NG. Activation of Akt is essential for the propagation of mitochondrial respiratory stress signaling and activation of the transcriptional coactivator heterogeneous ribonucleoprotein A2. Mol Biol Cell 2010; 21:3578-89. [PMID: 20719961 PMCID: PMC2954122 DOI: 10.1091/mbc.e10-03-0192] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This article shows that mitochondrial respiratory dysfunction activates a stress signaling that induces Akt1 activation. Akt1 activation occurs through calcineurin-mediated IGF1R/PI3-K pathway. Akt1-mediated phosphorylation of hnRNPA2 is a key requirement for the propagation of stress signaling and activation of nuclear target genes. Mitochondrial respiratory stress (also called mitochondrial retrograde signaling) activates a Ca2+/calcineurin-mediated signal that culminates in transcription activation/repression of a large number of nuclear genes. This signal is propagated through activation of the regulatory proteins NFκB c-Rel/p50, C/EBPδ, CREB, and NFAT. Additionally, the heterogeneous ribonucleoprotein A2 (hnRNPA2) functions as a coactivator in up-regulating the transcription of Cathepsin L, RyR1, and Glut-4, the target genes of stress signaling. Activation of IGF1R, which causes a metabolic switch to glycolysis, cell invasiveness, and resistance to apoptosis, is a phenotypic hallmark of C2C12 myoblasts subjected to mitochondrial stress. In this study, we report that mitochondrial stress leads to increased expression, activation, and nuclear localization of Akt1. Mitochondrial respiratory stress also activates Akt1-gene expression, which involves hnRNPA2 as a coactivator, indicating a complex interdependency of these two factors. Using Akt1−/− mouse embryonic fibroblasts and Akt1 mRNA-silenced C2C12 cells, we show that Akt1-mediated phosphorylation is crucial for the activation and recruitment of hnRNPA2 to the enhanceosome complex. Akt1 mRNA silencing in mtDNA-depleted cells resulted in reversal of the invasive phenotype, accompanied by sensitivity to apoptotic stimuli. These results show that Akt1 is an important regulator of the nuclear transcriptional response to mitochondrial stress.
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Affiliation(s)
- Manti Guha
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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31
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Tyynismaa H, Carroll CJ, Raimundo N, Ahola-Erkkilä S, Wenz T, Ruhanen H, Guse K, Hemminki A, Peltola-Mjøsund KE, Tulkki V, Oresic M, Moraes CT, Pietiläinen K, Hovatta I, Suomalainen A. Mitochondrial myopathy induces a starvation-like response. Hum Mol Genet 2010; 19:3948-58. [PMID: 20656789 DOI: 10.1093/hmg/ddq310] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial respiratory chain (RC) deficiency is among the most common causes of inherited metabolic disease, but its physiological consequences are poorly characterized. We studied the skeletal muscle gene expression profiles of mice with late-onset mitochondrial myopathy. These animals express a dominant patient mutation in the mitochondrial replicative helicase Twinkle, leading to accumulation of multiple mtDNA deletions and progressive subtle RC deficiency in the skeletal muscle. The global gene expression pattern of the mouse skeletal muscle showed induction of pathways involved in amino acid starvation response and activation of Akt signaling. Furthermore, the muscle showed induction of a fasting-related hormone, fibroblast growth factor 21 (Fgf21). This secreted regulator of lipid metabolism was also elevated in the mouse serum, and the animals showed widespread changes in their lipid metabolism: small adipocyte size, low fat content in the liver and resistance to high-fat diet. We propose that RC deficiency induces a mitochondrial stress response, with local and global changes mimicking starvation, in a normal nutritional state. These results may have important implications for understanding the metabolic consequences of mitochondrial myopathies.
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Affiliation(s)
- Henna Tyynismaa
- Research Program of Molecular Neurology, Biomedicum-Helsinki, 00290 Helsinki, Finland
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Ronchi D, Virgilio R, Bordoni A, Fassone E, Sciacco M, Ciscato P, Moggio M, Govoni A, Corti S, Bresolin N, Comi GP. The m.12316G>A mutation in the mitochondrial tRNA Leu(CUN) gene is associated with mitochondrial myopathy and respiratory impairment. J Neurol Sci 2010; 292:107-10. [PMID: 20163808 DOI: 10.1016/j.jns.2010.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 01/18/2010] [Accepted: 01/27/2010] [Indexed: 11/24/2022]
Abstract
Mitochondrial disorders are often associated with mutations in mitochondrial tRNA. Independent observation of the same molecular defect in unrelated subjects is a generally required proof of pathogenicity. A sporadic case of chronic external ophthalmoplegia (cPEO) with ragged red fibres (RRFs) has been previously related to an m.12316G>A substitution in tRNA(Leu(CUN)). Sequencing muscle-derived mtDNA, we found the m.12316G>A substitution in an adult woman with mitochondrial myopathy and respiratory impairment. Her muscle biopsy presented several cytochrome c oxidase-negative (COX-) fibres, and RRFs as signs of mitochondrial proliferation. Restriction-fragment length polymorphism (RFLP) analysis of the mutation in isolated muscle fibres showed a threshold of at least 60% of mutated mtDNA to determine a COX deficiency phenotype. This second report of the m.12316G>A mutation in a sporadic patient consolidates its pathogenic nature and provides further elements for genetic counselling.
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Affiliation(s)
- Dario Ronchi
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Foundation Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena, Milan, Italy
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Role of calcineurin, hnRNPA2 and Akt in mitochondrial respiratory stress-mediated transcription activation of nuclear gene targets. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1055-65. [PMID: 20153290 DOI: 10.1016/j.bbabio.2010.02.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/01/2010] [Accepted: 02/07/2010] [Indexed: 01/18/2023]
Abstract
Pathophysiological conditions causing mitochondrial dysfunction and altered transmembrane potential (psim) initiate a mitochondrial respiratory stress response, also known as mitochondrial retrograde response, in a variety of mammalian cells. An increase in the cytosolic Ca2+ [Ca2+]c as part of this signaling cascade activates Ca2+ responsive phosphatase, calcineurin (Cn). Activation of IGF1R accompanied by increased glycolysis, invasiveness, and resistance to apoptosis is a phenotypic hallmark of C2C12 skeletal muscle cells subjected to this stress. The signaling is associated with activation and increased nuclear translocation of a number of transcription factors including a novel NFkappaB (cRel:p50) pathway, NFAT, CREB and C/EBPdelta. This culminates in the upregulation of a number of nuclear genes including Cathepsin L, RyR1, Glut4 and Akt1. We observed that stress regulated transcription activation of nuclear genes involves a cooperative interplay between NFkappaB (cRel:p50), C/EBPdelta, CREB, and NFAT. Our results show that the functional synergy of these factors requires the stress-activated heterogeneous nuclear ribonucleoprotein, hnRNPA2 as a transcriptional coactivator. We report here that mitochondrial stress leads to induced expression and activation of serine threonine kinase Akt1. Interestingly, we observe that Akt1 phosphorylates hnRNPA2 under mitochondrial stress conditions, which is a crucial step for the recruitment of this coactivator to the stress target promoters and culmination in mitochondrial stress-mediated transcription activation of target genes. We propose that mitochondrial stress plays an important role in tumor progression and emergence of invasive phenotypes.
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Mitochondrial DNA mutations and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:113-28. [PMID: 19761752 DOI: 10.1016/j.bbabio.2009.09.005] [Citation(s) in RCA: 417] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 01/07/2023]
Abstract
Mitochondrial disorders are a group of clinically heterogeneous diseases, commonly defined by a lack of cellular energy due to oxidative phosphorylation (OXPHOS) defects. Since the identification of the first human pathological mitochondrial DNA (mtDNA) mutations in 1988, significant efforts have been spent in cataloguing the vast array of causative genetic defects of these disorders. Currently, more than 250 pathogenic mtDNA mutations have been identified. An ever-increasing number of nuclear DNA mutations are also being reported as the majority of proteins involved in mitochondrial metabolism and maintenance are nuclear-encoded. Understanding the phenotypic diversity and elucidating the molecular mechanisms at the basis of these diseases has however proved challenging. Progress has been hampered by the peculiar features of mitochondrial genetics, an inability to manipulate the mitochondrial genome, and difficulties in obtaining suitable models of disease. In this review, we will first outline the unique features of mitochondrial genetics before detailing the diseases and their genetic causes, focusing specifically on primary mtDNA genetic defects. The functional consequences of mtDNA mutations that have been characterised to date will also be discussed, along with current and potential future diagnostic and therapeutic advances.
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Mancuso M, Orsucci D, Ali G, Lo Gerfo A, Fontanini G, Siciliano G. Advances in molecular diagnostics for mitochondrial diseases. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2009; 3:557-569. [PMID: 23495985 DOI: 10.1517/17530050902967610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Mitochondrial disorders (MD) are diseases caused by impairment of the mitochondrial respiratory chain. Phenotypes are polymorphous and may range from pure myopathy to multisystemic disorders. The genetic defect can be located on mitochondrial or nuclear DNA. At present, diagnosis of MD requires a complex approach: measurement of serum lactate, electromyography, muscle histology and enzymology, and genetic analysis. Magnetic resonance spectroscopy allows the assessment of tissue metabolic alterations, thus providing useful information for the diagnosis and monitoring of MD. Molecular soluble markers of mitochondrial dysfunction, at rest and during exercise, can identify the impairment of the aerobic system in MD, but a reliable biomarker for the screening or diagnosis of MD is still needed. OBJECTIVE Molecular and genetic characterization of MD, together with other experimental approaches, contribute to add new insights to these diseases. Here, the role and advances of diagnostic techniques for MD are reviewed. CONCLUSION Possible applications of the results obtained by new molecular investigative approaches could in future guide therapeutic strategies.
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Affiliation(s)
- Michelangelo Mancuso
- University of Pisa, Neurological Clinic, Department of Neuroscience, Via Roma 67, 56126 Pisa, Italy +0039 050 992440 ; +0039 050 554808 ;
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Bykhovskaya Y, Mengesha E, Fischel-Ghodsian N. Phenotypic expression of maternally inherited deafness is affected by RNA modification and cytoplasmic ribosomal proteins. Mol Genet Metab 2009; 97:297-304. [PMID: 19482502 PMCID: PMC2728627 DOI: 10.1016/j.ymgme.2009.05.003] [Citation(s) in RCA: 7] [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: 03/30/2009] [Revised: 04/30/2009] [Accepted: 05/02/2009] [Indexed: 01/06/2023]
Abstract
The homoplasmic mitochondrial A1555G mutation in the 12S rRNA gene leads to a mitochondrial translation disorder associated with deafness. The absence of disease in non-cochlear tissues in all patients, and in the cochlea in some patients, is not well understood. We used a system-based approach, including whole genome expression and biological function analysis, to elucidate the pathways underlying tissue specificity and clinical severity of this condition. Levels of over 48K RNA transcripts from EBV-transformed lymphoblasts of deaf and hearing individuals with the A1555G mutation and controls were obtained. Differentially expressed transcripts were functionally grouped using gene set enrichment analysis. Over 50 RNA binding proteins were differentially expressed between deaf and hearing individuals with the A1555G mutation (P-value of 2.56E-7), confirming previous genetic data implicating this pathway in the determination of the severity of hearing loss. Unexpectedly, the majority of cytoplasmic ribosomal genes were up-regulated in a coordinated fashion in individuals with the A1555G mutation versus controls (P-value of 3.91E-135). This finding was verified through real time RT-PCR, and through measuring of protein levels by flow cytometry. Analysis of expression levels of other differentially expressed genes suggests that this coordinated over-expression of cytoplasmic ribosomal proteins might occur through the Myc/Max pathway. We propose that expression levels of RNA binding proteins help determine the severity of the cochlear phenotype, and that coordinated up-regulation of the cytoplasmic translation apparatus operates as a compensation mechanism in unaffected tissues of patients with maternal deafness associated with the A1555G mutation.
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Affiliation(s)
- Yelena Bykhovskaya
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
| | - Emebet Mengesha
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
| | - Nathan Fischel-Ghodsian
- Medical Genetics Institute, Ahmanson Department of Pediatrics, Steven Spielberg Pediatric Research Center, Cedars-Sinai Medical Center and David Geffen School of Medicine at UCLA, 8700 Beverly Blvd, Los Angeles, California, 90048 USA
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Guha M, Pan H, Fang JK, Avadhani NG. Heterogeneous nuclear ribonucleoprotein A2 is a common transcriptional coactivator in the nuclear transcription response to mitochondrial respiratory stress. Mol Biol Cell 2009; 20:4107-19. [PMID: 19641020 DOI: 10.1091/mbc.e09-04-0296] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial dysfunction and altered transmembrane potential initiate a mitochondrial respiratory stress response, also known as mitochondrial retrograde response, in a wide spectrum of cells. The mitochondrial stress response activates calcineurin, which regulates transcription factors, including a new nuclear factor-kappaB (NF-kappaB) pathway, different from the canonical and noncanonical pathways. In this study using a combination of small interfering RNA-mediated mRNA knock down, transcriptional analysis, and chromatin immunoprecipitation, we report a common mechanism for the regulation of previously established stress response genes Cathepsin L, RyR1, and Glut4. Stress-regulated transcription involves the cooperative interplay between NF-kappaB (cRel: p50), C/EBPdelta, cAMP response element-binding protein, and nuclear factor of activated T cells. We show that the functional synergy of these factors requires the stress-activated heterogeneous nuclear ribonucleoprotein (hnRNP) A2 as a coactivator. HnRNP A2 associates with the enhanceosome, mostly through protein-protein interactions with DNA-bound factors. Silencing of hnRNP A2 as well as other DNA binding signature factors prevents stress-induced transcriptional activation and reverses the invasiveness of mitochondrial DNA-depleted C2C12 cells. Induction of mitochondrial stress signaling by electron transfer chain inhibitors also involved hnRNPA2 activation. We describe a common mechanism of mitochondrial respiratory stress-induced activation of nuclear target genes that involves hnRNP A2 as a transcription coactivator.
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Affiliation(s)
- Manti Guha
- Department of Animal Biology and Marie Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Reinecke F, Smeitink JAM, van der Westhuizen FH. OXPHOS gene expression and control in mitochondrial disorders. Biochim Biophys Acta Mol Basis Dis 2009; 1792:1113-21. [PMID: 19389473 DOI: 10.1016/j.bbadis.2009.04.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 04/08/2009] [Accepted: 04/14/2009] [Indexed: 12/20/2022]
Abstract
The cellular consequences of deficiencies of the mitochondrial OXPHOS system include a variety of direct and secondary changes in metabolite homeostasis, such as ROS, Ca(2+), ADP/ATP, and NAD/NADH. The adaptive responses to these changes include the transcriptional responses of nuclear and mitochondrial genes that are mediated by these metabolites, control of the mitochondria permeability transition pore, and a great variety of secondary signalling elements. Among the transcriptional responses reported over more than a decade using material harboring mtDNA mutations, deletions, or depletions, nuclear and mitochondrial DNA OXPHOS genes have mostly been up-regulated. However, it is evident from the limited data in a variety of disease models that expression responses are highly diverse and inconsistent. In this article, the mechanisms and controlling elements of these transcriptional responses are reviewed. In addition, the elements that need to be evaluated, in order to gain an improved perspective of the manner in which OXPHOS genes respond and impact on mitochondrial disease expression, are highlighted.
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Affiliation(s)
- Fimmie Reinecke
- Centre for Human Metabonomics, School for Physical and Chemical Sciences, North-West University, Hoffman street, Potchefstroom 2531, South Africa
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Kadota K, Nakai Y, Shimizu K. A weighted average difference method for detecting differentially expressed genes from microarray data. Algorithms Mol Biol 2008; 3:8. [PMID: 18578891 PMCID: PMC2464587 DOI: 10.1186/1748-7188-3-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 06/26/2008] [Indexed: 01/05/2023] Open
Abstract
Background Identification of differentially expressed genes (DEGs) under different experimental conditions is an important task in many microarray studies. However, choosing which method to use for a particular application is problematic because its performance depends on the evaluation metric, the dataset, and so on. In addition, when using the Affymetrix GeneChip® system, researchers must select a preprocessing algorithm from a number of competing algorithms such as MAS, RMA, and DFW, for obtaining expression-level measurements. To achieve optimal performance for detecting DEGs, a suitable combination of gene selection method and preprocessing algorithm needs to be selected for a given probe-level dataset. Results We introduce a new fold-change (FC)-based method, the weighted average difference method (WAD), for ranking DEGs. It uses the average difference and relative average signal intensity so that highly expressed genes are highly ranked on the average for the different conditions. The idea is based on our observation that known or potential marker genes (or proteins) tend to have high expression levels. We compared WAD with seven other methods; average difference (AD), FC, rank products (RP), moderated t statistic (modT), significance analysis of microarrays (samT), shrinkage t statistic (shrinkT), and intensity-based moderated t statistic (ibmT). The evaluation was performed using a total of 38 different binary (two-class) probe-level datasets: two artificial "spike-in" datasets and 36 real experimental datasets. The results indicate that WAD outperforms the other methods when sensitivity and specificity are considered simultaneously: the area under the receiver operating characteristic curve for WAD was the highest on average for the 38 datasets. The gene ranking for WAD was also the most consistent when subsets of top-ranked genes produced from three different preprocessed data (MAS, RMA, and DFW) were compared. Overall, WAD performed the best for MAS-preprocessed data and the FC-based methods (AD, WAD, FC, or RP) performed well for RMA and DFW-preprocessed data. Conclusion WAD is a promising alternative to existing methods for ranking DEGs with two classes. Its high performance should increase researchers' confidence in microarray analyses.
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Morel F, Renoux M, Lachaume P, Alziari S. Bleomycin-induced double-strand breaks in mitochondrial DNA of Drosophila cells are repaired. Mutat Res 2007; 637:111-7. [PMID: 17825327 DOI: 10.1016/j.mrfmmm.2007.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 06/28/2007] [Accepted: 07/17/2007] [Indexed: 11/23/2022]
Abstract
Mitochondrial DNA lesions cause numerous human diseases, and it is therefore important to identify the mechanisms whereby the mitochondrion repairs the damage. We have studied in cultured Drosophila cells the repair of bleomycin-induced double-strand breaks (DSBs) in mitochondrial DNA. Our results show that DSBs are repaired as rapidly and effectively in the mitochondria as in the nucleus. DNA repair is complete within 2h following bleomycin treatment, showing that Drosophila mitochondria have an effective system of DSB repair. The mechanism and mitochondrial proteins involved remain to be identified.
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Affiliation(s)
- Frederic Morel
- Equipe Genome Mitochondrial, UMR CNRS 6547, Université Blaise-Pascal, Clermont 2, 63177, Aubière-Cedex, France
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Finsterer J. Genetic, pathogenetic, and phenotypic implications of the mitochondrial A3243G tRNALeu(UUR) mutation. Acta Neurol Scand 2007; 116:1-14. [PMID: 17587249 DOI: 10.1111/j.1600-0404.2007.00836.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Mitochondrial disorders are frequently caused by mutations in mitochondrial genes and usually present as multisystem disease. One of the most frequent mitochondrial mutations is the A3,243G transition in the tRNALeu(UUR) gene. The phenotypic expression of the mutation is variable and comprises syndromic or non-syndromic mitochondrial disorders. Among the syndromic manifestations the mitochondrial encephalopathy, lactacidosis, and stroke-like episode (MELAS) syndrome is the most frequent. In single cases the A3,243G mutation may be associated with maternally inherited diabetes and deafness syndrome, myoclonic epilepsy and ragged-red fibers (MERRF) syndrome, MELAS/MERRF overlap syndrome, maternally inherited Leigh syndrome, chronic external ophthalmoplegia, or Kearns-Sayre syndrome. The wide phenotypic variability of the mutation is explained by the peculiarities of the mitochondrial DNA, such as heteroplasmy and mitotic segregation, resulting in different mutation loads in different tissues and family members. Moreover, there is some evidence that additional mtDNA sequence variations (polymorphisms, haplotypes) influence the phenotype of the A3,243G mutation. This review aims to give an overview on the actual knowledge about the genetic, pathogenetic, and phenotypic implications of the A3,243G mtDNA mutation.
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Affiliation(s)
- J Finsterer
- Krankenanstalt Rudolfstiftung, Vienna, Austria.
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Mende S, Storch A, Reichmann H. [Gene expression profiling of classic mitochondrial disorders. Its value in finding therapeutic strategies]. DER NERVENARZT 2007; 78:1155-9. [PMID: 17458528 DOI: 10.1007/s00115-007-2266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mitochondria are semiautonomous cell organelles which possess their own genome (mtDNA) but nonetheless depend on the import of nuclear-encoded proteins. In recent years, several mutations of mtDNA have been associated with specific diseases of the muscles and nervous system. In 1993, the A>G point mutation at position 3243 of the mtDNA, until then a prominent genetic marker for mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), was detected in patients with progressive external ophthalmoplegia (PEO). Due to the divergent clinical presentations of MELAS and PEO, the presence of potential nuclear secondary mutations or so-called modifier genes had been suspected. Now it is well known that a bidirectional information flow between the mitochondrion and the cell nucleus exists and that nuclear gene expression adapts to the functional status of the mitochondria. However it remains unclear when and how the nucleus responds to changes or mutations of the mtDNA and if there are indeed disease-specific biomarker genes whose expression changes in case of mtDNA aberrations. This review article focuses on the most recent gene expression profiling studies in the field of classic mitochondrial disorders.
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Affiliation(s)
- S Mende
- Klinik und Poliklinik für Neurologie, Technische Universität Dresden.
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Fujita Y, Ito M, Nozawa Y, Yoneda M, Oshida Y, Tanaka M. CHOP (C/EBP homologous protein) and ASNS (asparagine synthetase) induction in cybrid cells harboring MELAS and NARP mitochondrial DNA mutations. Mitochondrion 2007; 7:80-8. [PMID: 17276738 DOI: 10.1016/j.mito.2006.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 10/19/2006] [Indexed: 10/23/2022]
Abstract
Mitochondrial dysfunction caused by mutations in mitochondrial DNA (mtDNA) is related to a variety of diseases including MELAS and NARP syndromes. However, little is known about the intracellular responses induced by mtDNA mutations. In order to identify genes whose expression is altered as a result of the presence of mtDNA mutations, DNA microarray analysis was performed using human 143B osteosarcoma cells harboring 3243A>G [tRNA-Leu (UUR)] and 8993T>G [ATPase6 Leu156Arg] mtDNA mutations associated with MELAS and NARP syndromes (2SD and NARP3-1 cybrid cells), respectively. We found that mRNA and protein levels of ATF4, CHOP and ASNS were upregulated in 2SD and NARP3-1 cells as compared with parental cells. Reporter assays demonstrated that transcription of CHOP and ASNS genes was upregulated through the AARE (amino acid regulatory element) and NSRE-1 (nutrient-sensing response element-1) enhancer elements to which ATF4 binds, respectively. Furthermore, knockdown of ATF4 by RNA interference reduced CHOP and ASNS transcription in 2SD and NARP3-1 cells. These results suggest that the presence of mtDNA mutations elicits upregulation of CHOP and ASNS genes through the elevation of ATF4 expression and its binding to the AARE and NSRE-1, respectively.
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Affiliation(s)
- Yasunori Fujita
- Department of Longevity and Aging Research, Gifu International Institute of Biotechnology, 1-1 Naka-Fudogaoka, Kakamigahara, Gifu 504-0838, Japan
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Abstract
PURPOSE OF REVIEW Our understanding of mitochondrial diseases (defined restrictively as defects of the mitochondrial respiratory chain) is expanding rapidly. In this review, I will give the latest information on disorders affecting predominantly or exclusively skeletal muscle. RECENT FINDINGS The most recently described mitochondrial myopathies are due to defects in nuclear DNA, including coenzyme Q10 deficiency and mutations in genes controlling mitochondrial DNA abundance and structure, such as POLG, TK2, and MPV17. Barth syndrome, an X-linked recessive mitochondrial myopathy/cardiopathy, is associated with decreased amount and altered structure of cardiolipin, the main phospholipid of the inner mitochondrial membrane, but a secondary impairment of respiratory chain function is plausible. The role of mutations in protein-coding genes of mitochondrial DNA in causing isolated myopathies has been confirmed. Mutations in tRNA genes of mitochondrial DNA can also cause predominantly myopathic syndromes and--contrary to conventional wisdom--these mutations can be homoplasmic. SUMMARY Defects in the mitochondrial respiratory chain impair energy production and almost invariably involve skeletal muscle, causing exercise intolerance, cramps, recurrent myoglobinuria, or fixed weakness, which often affects extraocular muscles and results in droopy eyelids (ptosis) and progressive external ophthalmoplegia.
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Affiliation(s)
- Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA.
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Szustakowski JD, Lee JH, Marrese CA, Kosinski PA, Nirmala NR, Kemp DM. Identification of novel pathway regulation during myogenic differentiation. Genomics 2006; 87:129-38. [PMID: 16300922 DOI: 10.1016/j.ygeno.2005.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Accepted: 08/23/2005] [Indexed: 11/24/2022]
Abstract
Stem cell differentiation is governed by extracellular signals that activate intracellular networks (or pathways) to drive phenotypic specification. Using a novel gene clustering strategy we determined pathway relationships from a genome-wide transcriptional dataset of skeletal myoblast differentiation. Established myogenic pathways, including cell contractility and cell-cycle arrest, were predicted with extreme statistical significance (p approximately 0). In addition, gene sets associated with angiogenesis, neuronal activity, and mRNA splicing were regulated, exposing developmental and therapeutic implications. Acquisition of transcriptional data spanning the entire differentiation time course provided context for a dynamic landscape of functional pathway regulation. This novel perspective on myogenic cell differentiation revealed previously unrecognized patterns of regulation. We predict that similar analyses will facilitate ongoing efforts to define molecular mechanisms in other stem cell and developmental paradigms. Finally, by combining an iterative process of analysis with supplementation of novel pathways, this application may evolve into a powerful discovery tool.
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Affiliation(s)
- Joseph D Szustakowski
- Life Science Informatics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
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Crimi M, O'Hearn SF, Wallace DC, Comi GP. Molecular research technologies in mitochondrial diseases: The microarray approach. IUBMB Life 2005; 57:811-8. [PMID: 16393784 DOI: 10.1080/15216540500460269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mitochondria are ubiquitous in eukaryotic cells where they generate much of the cellular energy by the process of oxidative phosphorylation (OXPHOS). The approximately 1500 genes of the mitochondrial genome are distributed between the cytoplasmic, maternally-inherited, mitochondrial DNA (mtDNA) which encodes 37 genes and the nuclear DNA (nDNA) which encompasses the remaining mitochondrial genes. The interplay between the mtDNA and nDNA encoded mitochondrial genes and their role in mitochondrial disorders is still largely unclear. One approach for elucidating the pathophysiology of mitochondrial diseases has been to look at changes in the expression of mtDNA and nDNA-encoded genes in response to specific mitochondrial genetic defects. Initial studies of gene expression changes in response to mtDNA defect employed blot technologies to analyze changes in the expression of individual genes one at a time. While Southern/Northern blot experiments confirmed the importance of nDNA-mtDNA interactions in the pathophysiology of mitochondrial myopathy, the methodology used limited the number of genes that could be analyzed from each patient. This barrier has been overcome, in part by the advent of DNA microarray technology. In DNA microarrays gene sequences or oligonucleotides homologous to gene sequences are arrayed on a solid support. The RNA from the subject is then isolated, the mRNA converted to cDNA and the cDNA labeled with a fluorescent probe. The labeled cDNA is hybridized on the microarray and the fluorescence bound to each array is then quantified. Recently, these technologies have been applied to mitochondrial disease patient tissues and the presence of coordinate changes in mitochondrial gene expression confirmed.
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Affiliation(s)
- Marco Crimi
- Center for Molecular and Mitochondrial Medicine and Genetics, Department of Biological Chemistry, University of California, Irvine, California 92697-3940, USA.
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Jazwinski SM. Rtg2 protein: at the nexus of yeast longevity and aging. FEMS Yeast Res 2005; 5:1253-9. [PMID: 16099222 DOI: 10.1016/j.femsyr.2005.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 06/28/2005] [Accepted: 07/01/2005] [Indexed: 10/25/2022] Open
Abstract
Firm support for the notion that metabolism and particularly mitochondrial metabolism plays a significant role in aging has been gathered in studies on yeast. As in other organisms, mitochondria contribute to aging through their propensity to generate reactive oxygen species. There is more to the involvement of mitochondria in aging than this, however. Mitochondrial dysfunction, which accumulates during aging, triggers the retrograde response, an intracellular signaling pathway that activates genes that compensate for this dysfunction. A key signaling protein in this pathway is the Rtg2 protein. Recent studies have provided evidence that this protein lies at the nexus of the four major processes that are involved in aging in yeast and in other organisms; namely, metabolism, stress resistance, chromatin-dependent gene regulation, and genome stability. The details of this central role of Rtg2 protein explain the delicate balance between longevity and aging, which ultimately must tip towards the latter. Phenomena that resemble the retrograde response appear to exist in human cells, with both common and cell type-specific gene expression changes as the output.
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Affiliation(s)
- S Michal Jazwinski
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1901 Perdido St., P.O. Box P7-2, New Orleans, LA 70112, USA.
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