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Protasoni M, Taanman JW. Remodelling of the Mitochondrial Bioenergetic Pathways in Human Cultured Fibroblasts with Carbohydrates. BIOLOGY 2023; 12:1002. [PMID: 37508431 PMCID: PMC10376623 DOI: 10.3390/biology12071002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mitochondrial oxidative phosphorylation defects underlie many neurological and neuromuscular diseases. Patients' primary dermal fibroblasts are one of the most commonly used in vitro models to study mitochondrial pathologies. However, fibroblasts tend to rely more on glycolysis than oxidative phosphorylation for their energy when cultivated in standard high-glucose medium, rendering it difficult to expose mitochondrial dysfunctions. This study aimed to systematically investigate to which extent the use of galactose- or fructose-based medium switches the fibroblasts' energy metabolism to a more oxidative state. Highly proliferative cells depend more on glycolysis than less proliferative cells. Therefore, we investigated two primary dermal fibroblast cultures from healthy subjects: a highly proliferative neonatal culture and a slower-growing adult culture. Cells were cultured with 25 mM glucose, galactose or fructose, and 4 mM glutamine as carbon sources. Compared to glucose, both galactose and fructose reduce the cellular proliferation rate, but the galactose-induced drop in proliferation is much more profound than the one observed in cells cultivated in fructose. Both galactose and fructose result in a modest increase in mitochondrial content, including mitochondrial DNA, and a disproportionate increase in protein levels, assembly, and activity of the oxidative phosphorylation enzyme complexes. Galactose- and fructose-based media induce a switch of the prevalent biochemical pathway in cultured fibroblasts, enhancing aerobic metabolism when compared to glucose-based medium. While both galactose and fructose stimulate oxidative phosphorylation to a comparable degree, galactose decreases the cellular proliferation rate more than fructose, suggesting that a fructose-based medium is a better choice when studying partial oxidative phosphorylation defects in patients' fibroblasts.
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Affiliation(s)
- Margherita Protasoni
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, Royal Free Campus (M12), Rowland Hill Street, London NW3 2PF, UK
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, Royal Free Campus (M12), Rowland Hill Street, London NW3 2PF, UK
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2
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Pinho SA, Costa CF, Deus CM, Pinho SLC, Miranda‐Santos I, Afonso G, Bagshaw O, Stuart JA, Oliveira PJ, Cunha‐Oliveira T. Mitochondrial and metabolic remodelling in human skin fibroblasts in response to glucose availability. FEBS J 2022; 289:5198-5217. [DOI: 10.1111/febs.16413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/01/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Sónia A. Pinho
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB) Institute for Interdisciplinary Research (IIIUC) University of Coimbra Portugal
| | - Cláudio F. Costa
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Cláudia M. Deus
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Sonia L. C. Pinho
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
- CIVG‐ Vasco da Gama Research Center Vasco da Gama University School Portugal
| | - Inês Miranda‐Santos
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Gonçalo Afonso
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Olivia Bagshaw
- Department of Biological Sciences Brock University St. Catharines ON Canada
| | - Jeffrey A. Stuart
- Department of Biological Sciences Brock University St. Catharines ON Canada
| | - Paulo J. Oliveira
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Teresa Cunha‐Oliveira
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
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3
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Sahebekhtiari N, Fernandez-Guerra P, Nochi Z, Carlsen J, Bross P, Palmfeldt J. Deficiency of the mitochondrial sulfide regulator ETHE1 disturbs cell growth, glutathione level and causes proteome alterations outside mitochondria. Biochim Biophys Acta Mol Basis Dis 2018; 1865:126-135. [PMID: 30391543 DOI: 10.1016/j.bbadis.2018.10.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/14/2018] [Accepted: 10/30/2018] [Indexed: 01/15/2023]
Abstract
The mitochondrial enzyme ETHE1 is a persulfide dioxygenase essential for cellular sulfide detoxification, and its deficiency causes the severe and complex inherited metabolic disorder ethylmalonic encephalopathy (EE). In spite of well-described clinical symptoms of the disease, detailed cellular and molecular characterization is still ambiguous. Cellular redox regulation has been described to be influenced in ETHE1 deficient cells, and to clarify this further we applied image cytometry and detected decreased levels of reduced glutathione (GSH) in cultivated EE patient fibroblast cells. Cell growth initiation of the EE patient cells was impaired, whereas cell cycle regulation was not. Furthermore, Seahorse metabolic analyzes revealed decreased extracellular acidification, i. e. decreased lactate formation from glycolysis, in the EE patient cells. TMT-based large-scale proteomics was subsequently performed to broadly elucidate cellular consequences of the ETHE1 deficiency. More than 130 proteins were differentially regulated, of which the majority were non-mitochondrial. The proteomics data revealed a link between ETHE1-deficiency and down-regulation of several ribosomal proteins and LIM domain proteins important for cellular maintenance, and up-regulation of cell surface glycoproteins. Furthermore, several proteins of endoplasmic reticulum (ER) were perturbed including proteins influencing disulfide bond formation (e.g. protein disulfide isomerases and peroxiredoxin 4) and calcium-regulated proteins. The results indicate that decreased level of reduced GSH and alterations in proteins of ribosomes, ER and of cell adhesion lie behind the disrupted cell growth of the EE patient cells.
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Affiliation(s)
- Navid Sahebekhtiari
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Paula Fernandez-Guerra
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Zahra Nochi
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Jasper Carlsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Peter Bross
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.
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4
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Magri S, Fracasso V, Plumari M, Alfei E, Ghezzi D, Gellera C, Rusmini P, Poletti A, Di Bella D, Elia AE, Pantaleoni C, Taroni F. Concurrent AFG3L2 and SPG7 mutations associated with syndromic parkinsonism and optic atrophy with aberrant OPA1 processing and mitochondrial network fragmentation. Hum Mutat 2018; 39:2060-2071. [PMID: 30252181 DOI: 10.1002/humu.23658] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 09/03/2018] [Accepted: 09/22/2018] [Indexed: 01/26/2023]
Abstract
Mitochondrial dynamics and quality control are crucial for neuronal survival and their perturbation is a major cause of neurodegeneration. m-AAA complex is an ATP-dependent metalloprotease located in the inner mitochondrial membrane and involved in protein quality control. Mutations in the m-AAA subunits AFG3L2 and paraplegin are associated with autosomal dominant spinocerebellar ataxia (SCA28) and autosomal recessive hereditary spastic paraplegia (SPG7), respectively. We report a novel m-AAA-associated phenotype characterized by early-onset optic atrophy with spastic ataxia and L-dopa-responsive parkinsonism. The proband carried a de novo AFG3L2 heterozygous mutation (p.R468C) along with a heterozygous maternally inherited intragenic deletion of SPG7. Functional analysis in yeast demonstrated the pathogenic role of AFG3L2 p.R468C mutation shedding light on its pathogenic mechanism. Analysis of patient's fibroblasts showed an abnormal processing pattern of OPA1, a dynamin-related protein essential for mitochondrial fusion and responsible for most cases of hereditary optic atrophy. Consistently, assessment of mitochondrial morphology revealed a severe fragmentation of the mitochondrial network, not observed in SCA28 and SPG7 patients' cells. This case suggests that coincidental mutations in both components of the mitochondrial m-AAA protease may result in a complex phenotype and reveals a crucial role for OPA1 processing in the pathogenesis of neurodegenerative disease caused by m-AAA defects.
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Affiliation(s)
- Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valentina Fracasso
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Massimo Plumari
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Enrico Alfei
- Unit of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Paola Rusmini
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milan, Italy
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milan, Italy
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Antonio E Elia
- Unit of Neurology 1, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Unit of Developmental Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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5
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Edhager AV, Povlsen JA, Løfgren B, Bøtker HE, Palmfeldt J. Proteomics of the Rat Myocardium during Development of Type 2 Diabetes Mellitus Reveals Progressive Alterations in Major Metabolic Pathways. J Proteome Res 2018; 17:2521-2532. [PMID: 29847139 DOI: 10.1021/acs.jproteome.8b00276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Congestive heart failure and poor clinical outcome after myocardial infarction are known complications in patients with type-2 diabetes mellitus (T2DM). Protein alterations may be involved in the mechanisms underlying these disarrays in the diabetic heart. Here we map proteins involved in intracellular metabolic pathways in the Zucker diabetic fatty rat heart as T2DM develops using MS based proteomics. The prediabetic state only induced minor pathway changes, whereas onset and late T2DM caused pronounced perturbations. Two actin-associated proteins, ARPC2 and TPM3, were up-regulated at the prediabetic state indicating increased actin dynamics. All differentially regulated proteins involved in fatty acid metabolism, both peroxisomal and mitochondrial, were up-regulated at late T2DM, whereas enzymes of branched chain amino acid degradation were all down-regulated. At both onset and late T2DM, two members of the serine protease inhibitor superfamily, SERPINA3K and SERPINA3L, were down-regulated. Furthermore, we found alterations in proteins involved in clearance of advanced glycation end-products and lipotoxicity, DCXR and CBR1, at both onset and late T2DM. These proteins deserve elucidation with regard to their role in T2DM pathogenesis and their respective role in the deterioration of the diabetic heart. Data are available via ProteomeXchange with identifiers PXD009538, PXD009554, and PXD009555.
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Affiliation(s)
- Anders Valdemar Edhager
- Research Unit for Molecular Medicine, Department of Clinical Medicine , Aarhus University and Aarhus University Hospital , 8200 , Aarhus N , Denmark
| | | | - Bo Løfgren
- Department of Cardiology , Aarhus University Hospital , 8200 , Aarhus N , Denmark.,Institute for Experimental Clinical Research , Aarhus University , 8000 , Aarhus C , Denmark
| | - Hans Erik Bøtker
- Department of Cardiology , Aarhus University Hospital , 8200 , Aarhus N , Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine , Aarhus University and Aarhus University Hospital , 8200 , Aarhus N , Denmark
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6
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Selected reaction monitoring mass spectrometry for relative quantification of proteins involved in cellular life and death processes. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1035:49-56. [DOI: 10.1016/j.jchromb.2016.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022]
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7
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Parente MK, Rozen R, Seeholzer SH, Wolfe JH. Integrated analysis of proteome and transcriptome changes in the mucopolysaccharidosis type VII mouse hippocampus. Mol Genet Metab 2016; 118:41-54. [PMID: 27053151 PMCID: PMC4832927 DOI: 10.1016/j.ymgme.2016.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/05/2016] [Indexed: 12/15/2022]
Abstract
Mucopolysaccharidosis type VII (MPS VII) is a lysosomal storage disease caused by the deficiency of β-glucuronidase. In this study, we compared the changes relative to normal littermates in the proteome and transcriptome of the hippocampus in the C57Bl/6 mouse model of MPS VII, which has well-documented histopathological and neurodegenerative changes. A completely different set of significant changes between normal and MPS VII littermates were found in each assay. Nevertheless, the functional annotation terms generated by the two methods showed agreement in many of the processes, which also corresponded to known pathology associated with the disease. Additionally, assay-specific changes were found, which in the proteomic analysis included mitochondria, energy generation, and cytoskeletal differences in the mutant, while the transcriptome differences included immune, vesicular, and extracellular matrix changes. In addition, the transcriptomic changes in the mutant hippocampus were concordant with those in a MPS VII mouse caused by the same mutation but on a different background inbred strain.
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Affiliation(s)
- Michael K Parente
- Research Institute of the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ramona Rozen
- Research Institute of the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven H Seeholzer
- Research Institute of the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John H Wolfe
- Research Institute of the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; W. F. Goodman Center for Comparative Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Fernandez-Guerra P, Lund M, Corydon TJ, Cornelius N, Gregersen N, Palmfeldt J, Bross P. Application of an Image Cytometry Protocol for Cellular and Mitochondrial Phenotyping on Fibroblasts from Patients with Inherited Disorders. JIMD Rep 2015; 27:17-26. [PMID: 26404456 DOI: 10.1007/8904_2015_494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/13/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022] Open
Abstract
Cellular phenotyping of human dermal fibroblasts (HDFs) from patients with inherited diseases provides invaluable information for diagnosis, disease aetiology, prognosis and assessing of treatment options. Here we present a cell phenotyping protocol using image cytometry that combines measurements of crucial cellular and mitochondrial parameters: (1) cell number and viability, (2) thiol redox status (TRS), (3) mitochondrial membrane potential (MMP) and (4) mitochondrial superoxide levels (MSLs). With our protocol, cell viability, TRS and MMP can be measured in one small cell sample and MSL on a parallel one. We analysed HDFs from healthy individuals after treatment with various concentrations of hydrogen peroxide (H2O2) for different intervals, to mimic the physiological effects of oxidative stress. Our results show that cell number, viability, TRS and MMP decreased, while MSL increased both in a time- and concentration-dependent manner. To assess the use of our protocol for analysis of HDFs from patients with inherited diseases, we analysed HDFs from two patients with very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD), one with a severe clinical phenotype and one with a mild one. HDFs from both patients displayed increased MSL without H2O2 treatment. Treatment with H2O2 revealed significant differences in MMP and MSL between HDFs from the mild and the severe patient. Our results establish the capacity of our protocol for fast analysis of cellular and mitochondrial parameters by image cytometry in HDFs from patients with inherited metabolic diseases.
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Affiliation(s)
- Paula Fernandez-Guerra
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark.
| | - M Lund
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark
| | - T J Corydon
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - N Cornelius
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark.,Department of clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - N Gregersen
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark
| | - J Palmfeldt
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark
| | - Peter Bross
- Department of Clinical Medicine, Research Unit for Molecular Medicine (MMF), Aarhus University Hospital, Brendstrupgaardsvej 100, 8200, Aarhus, Denmark.
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9
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Komulainen T, Lodge T, Hinttala R, Bolszak M, Pietilä M, Koivunen P, Hakkola J, Poulton J, Morten KJ, Uusimaa J. Sodium valproate induces mitochondrial respiration dysfunction in HepG2 in vitro cell model. Toxicology 2015; 331:47-56. [PMID: 25745980 DOI: 10.1016/j.tox.2015.03.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 12/24/2022]
Abstract
Sodium valproate (VPA) is a potentially hepatotoxic antiepileptic drug. Risk of VPA-induced hepatotoxicity is increased in patients with mitochondrial diseases and especially in patients with POLG1 gene mutations. We used a HepG2 cell in vitro model to investigate the effect of VPA on mitochondrial activity. Cells were incubated in glucose medium and mitochondrial respiration-inducing medium supplemented with galactose and pyruvate. VPA treatments were carried out at concentrations of 0-2.0mM for 24-72 h. In both media, VPA caused decrease in oxygen consumption rates and mitochondrial membrane potential. VPA exposure led to depleted ATP levels in HepG2 cells incubated in galactose medium suggesting dysfunction in mitochondrial ATP production. In addition, VPA exposure for 72 h increased levels of mitochondrial reactive oxygen species (ROS), but adversely decreased protein levels of mitochondrial superoxide dismutase SOD2, suggesting oxidative stress caused by impaired elimination of mitochondrial ROS and a novel pathomechanism related to VPA toxicity. Increased cell death and decrease in cell number was detected under both metabolic conditions. However, immunoblotting did not show any changes in the protein levels of the catalytic subunit A of mitochondrial DNA polymerase γ, the mitochondrial respiratory chain complexes I, II and IV, ATP synthase, E3 subunit dihydrolipoyl dehydrogenase of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and glutathione peroxidase. Our results show that VPA inhibits mitochondrial respiration and leads to mitochondrial dysfunction, oxidative stress and increased cell death, thus suggesting an essential role of mitochondria in VPA-induced hepatotoxicity.
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Affiliation(s)
- Tuomas Komulainen
- PEDEGO Research Center and Medical Research Center Oulu, P.O. Box 5000, FIN-90014, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland.
| | - Tiffany Lodge
- Nuffield Department of Obstetrics and Gynaecology, Women's Centre, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX6 9DU, United Kingdom
| | - Reetta Hinttala
- PEDEGO Research Center and Medical Research Center Oulu, P.O. Box 5000, FIN-90014, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland
| | - Maija Bolszak
- PEDEGO Research Center and Medical Research Center Oulu, P.O. Box 5000, FIN-90014, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland
| | - Mika Pietilä
- Faculty of Medicine, Institute of Biomedicine, Department of Anatomy and Cell Biology, P.O. Box 5000, FI-90014, University of Oulu, Oulu, Finland
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemisty and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, P.O. Box 5400, FI-90014, University of Oulu, Finland
| | - Jukka Hakkola
- Faculty of Medicine, Institute of Biomedicine, Department of Pharmacology and Toxicology, P.O. Box 5000, FI-90014, University of Oulu, Oulu, Finland; Medical Research Center Oulu, P.O. Box 5000, FIN-90014, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Joanna Poulton
- Nuffield Department of Obstetrics and Gynaecology, Women's Centre, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX6 9DU, United Kingdom
| | - Karl J Morten
- Nuffield Department of Obstetrics and Gynaecology, Women's Centre, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX6 9DU, United Kingdom
| | - Johanna Uusimaa
- PEDEGO Research Center and Medical Research Center Oulu, P.O. Box 5000, FIN-90014, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland
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10
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Wang J, Yang J, Mao S, Chai X, Hu Y, Hou X, Tang Y, Bi C, Li X. MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PLoS One 2014; 9:e111187. [PMID: 25347823 PMCID: PMC4210245 DOI: 10.1371/journal.pone.0111187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 09/26/2014] [Indexed: 12/18/2022] Open
Abstract
Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of complicated biological mechanisms underlying mitochondrial functions and human mitochondrial diseases. MitProNet is freely accessible at http://bio.scu.edu.cn:8085/MitProNet.
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Affiliation(s)
- Jiabin Wang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Jian Yang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Song Mao
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xiaoqiang Chai
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Yuling Hu
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xugang Hou
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Yiheng Tang
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Cheng Bi
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
| | - Xiao Li
- College of Life Sciences, Sichuan University, Ministry of Education Key Laboratory for Bio-resource and Eco-environment, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, People’s Republic of China
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11
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Fernández-Guerra P, Birkler RID, Merinero B, Ugarte M, Gregersen N, Rodríguez-Pombo P, Bross P, Palmfeldt J. Selected reaction monitoring as an effective method for reliable quantification of disease-associated proteins in maple syrup urine disease. Mol Genet Genomic Med 2014; 2:383-92. [PMID: 25333063 PMCID: PMC4190873 DOI: 10.1002/mgg3.88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/25/2014] [Accepted: 04/29/2014] [Indexed: 12/15/2022] Open
Abstract
Selected reaction monitoring (SRM) mass spectrometry can quantitatively measure proteins by specific targeting of peptide sequences, and allows the determination of multiple proteins in one single analysis. Here, we show the feasibility of simultaneous measurements of multiple proteins in mitochondria-enriched samples from cultured fibroblasts from healthy individuals and patients with mutations in branched-chain α-ketoacid dehydrogenase (BCKDH) complex. BCKDH is a mitochondrial multienzyme complex and its defective activity causes maple syrup urine disease (MSUD), a rare but severe inherited metabolic disorder. Four different genes encode the catalytic subunits of BCKDH: E1α (BCKDHA), E1β (BCKDHB), E2 (DBT), and E3 (DLD). All four proteins were successfully quantified in healthy individuals. However, the E1α and E1β proteins were not detected in patients carrying mutations in one of those genes, whereas mRNA levels were almost unaltered, indicating instability of E1α and E1β monomers. Using SRM we elucidated the protein effects of mutations generating premature termination codons or misfolded proteins. SRM is a complement to transcript level measurements and a valuable tool to shed light on molecular mechanisms and on effects of pharmacological therapies at protein level. SRM is particularly effective for inherited disorders caused by multiple proteins such as defects in multienzyme complexes.
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Affiliation(s)
- Paula Fernández-Guerra
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Rune I D Birkler
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Centro de Investigación en Red de Enfermedades Raras (CIBERER), IDIPAZ, Universidad Autónoma Madrid Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Centro de Investigación en Red de Enfermedades Raras (CIBERER), IDIPAZ, Universidad Autónoma Madrid Madrid, Spain
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Pilar Rodríguez-Pombo
- Dpto Biol. Mol., Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Centro de Investigación en Red de Enfermedades Raras (CIBERER), IDIPAZ, Universidad Autónoma Madrid Madrid, Spain
| | - Peter Bross
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
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12
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Stødkilde L, Palmfeldt J, Nilsson L, Carlsen I, Wang Y, Nørregaard R, Frøkiaer J. Proteomic identification of early changes in the renal cytoskeleton in obstructive uropathy. Am J Physiol Renal Physiol 2014; 306:F1429-41. [PMID: 24761003 DOI: 10.1152/ajprenal.00244.2013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bilateral ureteral obstruction (BUO) is associated with renal damage and impaired ability to concentrate urine and is known to induce alterations in an array of kidney proteins. The aim of this study was to identify acute proteomic alterations induced by BUO. Rats were subjected to BUO for 2, 6, or 24 h. Mass spectrometry-based proteomics was performed on the renal inner medulla, and protein changes in the obstructed group were identified. Significant changes were successfully identified for 109 proteins belonging to different biological classes. Interestingly, proteins belonging to the cytoskeleton and proteins related to cytoskeletal regulation were found to be biologically enriched in BUO using online-accessible tools. Western blots confirmed the selected results, demonstrating acute downregulation of proteins belonging to all three cytoskeletal components. The microfilament protein β-actin and the intermediate filament proteins pankeratin and vimentin were all downregulated. β-Tubulin, an important microtubular protein, was found to be significantly downregulated after 24 h. Also, there was significant upregulation of cofilin, an actin-binding protein known to be upregulated in other nephropathy models. Furthermore, both upregulation and downregulation of cytoskeletal motor and regulatory proteins were observed. These findings were confirmed by immunohistochemistry, which clearly showed alterations in labeling in the inner medulla. Interestingly, we were able to confirm selected results in mpkCCD cells exposed to mechanical stretch. Our findings add to the knowledge of BUO-induced acute changes in the renal cytoskeleton and suggest that these molecular changes are partly mediated by increased stretch of the cells during obstruction.
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Affiliation(s)
- Lene Stødkilde
- Department of Clinical Physiology and Molecular Imaging, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; and Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Line Nilsson
- Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Inge Carlsen
- Department of Clinical Physiology and Molecular Imaging, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Yan Wang
- Department of Clinical Physiology and Molecular Imaging, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Nørregaard
- Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Frøkiaer
- Department of Clinical Physiology and Molecular Imaging, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine Aarhus University Hospital, Aarhus, Denmark
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13
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Edhager AV, Stenbroen V, Nielsen NS, Bross P, Olsen RKJ, Gregersen N, Palmfeldt J. Proteomic investigation of cultivated fibroblasts from patients with mitochondrial short-chain acyl-CoA dehydrogenase deficiency. Mol Genet Metab 2014; 111:360-368. [PMID: 24485985 DOI: 10.1016/j.ymgme.2014.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 12/23/2022]
Abstract
Short-chain acyl-CoA dehydrogenase (SCAD) deficiency is a rare inherited autosomal recessive disorder with not yet well established mechanisms of disease. In the present study, the mitochondrial proteome of five symptomatic patients homozygous for missense variations in the SCAD gene ACADS was investigated in an extensive large-scale proteomic study to map protein perturbations linked to the disease. Fibroblast cultures of patient cells homozygous for either c.319C>T/p.Arg107Cys (n=2) or c.1138C>T/p.Arg380Trp (n=3) in ACADS, and healthy controls (normal human dermal fibroblasts), were studied. The mitochondrial proteome derived from these cultures was analyzed by label free proteomics using high mass accuracy nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS). More than 300 mitochondrial proteins were identified and quantified. Thirteen proteins had significant alteration in protein levels in patients carrying variation c.319C>T in ACADS compared to controls and they belonged to various pathways, such as the antioxidant system and amino acid metabolism. Twenty-two proteins were found significantly altered in patients carrying variation c.1138C>T which included proteins associated with fatty acid β-oxidation, amino acid metabolism and protein quality control system. Three proteins were found significantly regulated in both patient groups: adenylate kinase 4 (AK4), nucleoside diphosphate kinase A (NME1) and aldehyde dehydrogenase family 4 member A1 (ALDH4A1). Proteins AK4 and NME1 deserve further investigation because of their involvement in energy reprogramming, cell survival and proliferation with relevance for SCAD deficiency and related metabolic disorders.
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Affiliation(s)
- Anders V Edhager
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Vibeke Stenbroen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Nadia Sukusu Nielsen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Bross
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke K J Olsen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
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14
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Modulation of mitochondrial bioenergetics in a skeletal muscle cell line model of mitochondrial toxicity. Redox Biol 2014; 2:224-33. [PMID: 24494197 PMCID: PMC3909783 DOI: 10.1016/j.redox.2013.12.028] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 12/24/2013] [Accepted: 12/24/2013] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial toxicity is increasingly being implicated as a contributing factor to many xenobiotic-induced organ toxicities, including skeletal muscle toxicity. This has necessitated the need for predictive in vitro models that are able to sensitively detect mitochondrial toxicity of chemical entities early in the research and development process. One such cell model involves substituting galactose for glucose in the culture media. Since cells cultured in galactose are unable to generate sufficient ATP from glycolysis they are forced to rely on mitochondrial oxidative phosphorylation for ATP generation and consequently are more sensitive to mitochondrial perturbation than cells grown in glucose. The aim of this study was to characterise cellular growth, bioenergetics and mitochondrial toxicity of the L6 rat skeletal muscle cell line cultured in either high glucose or galactose media. L6 myoblasts proliferated more slowly when cultured in galactose media, although they maintained similar levels of ATP. Galactose cultured L6 cells were significantly more sensitive to classical mitochondrial toxicants than glucose-cultured cells, confirming the cells had adapted to galactose media. Analysis of bioenergetic function with the XF Seahorse extracellular flux analyser demonstrated that oxygen consumption rate (OCR) was significantly increased whereas extracellular acidification rate (ECAR), a measure of glycolysis, was decreased in cells grown in galactose. Mitochondria operated closer to state 3 respiration and had a lower mitochondrial membrane potential and basal mitochondrial O2•– level compared to cells in the glucose model. An antimycin A (AA) dose response revealed that there was no difference in the sensitivity of OCR to AA inhibition between glucose and galactose cells. Importantly, cells in glucose were able to up-regulate glycolysis, while galactose cells were not. These results confirm that L6 cells are able to adapt to growth in a galactose media model and are consequently more susceptible to mitochondrial toxicants. L6 cells grown in glucose and galactose as model to detect skeletal muscle mitochondrial toxicity. L6 cells grown in galactose rely on mitochondrial oxidative phosphorylation for ATP production. Galactose cells are unable to use glycolysis to produce ATP following mitochondrial inhibition.
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Key Words
- AA, antimycin A
- ANT, adenine nucleotide translocase
- CPD, cumulative population doublings
- ECAR, extracellular acidification rate
- ETC, electron transport chain
- Extracellular flux analysis
- FCCP, Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone
- FSC, forward scatter
- Galactose
- Mitochondria
- O2•–, superoxide
- OCR, oxygen consumption rate
- OXPHOS, oxidative phosphorylation
- Oligo, oligomycin
- PD, population doublings
- PPP, pentose phosphate pathway
- RCR, respiratory control ratio
- SSC, side scatter
- Skeletal muscle toxicity
- TCA, tricarboxylic acid cycle
- UCPs, uncoupling proteins
- XF, extracellular flux
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15
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Elkalaf M, Anděl M, Trnka J. Low glucose but not galactose enhances oxidative mitochondrial metabolism in C2C12 myoblasts and myotubes. PLoS One 2013; 8:e70772. [PMID: 23940640 PMCID: PMC3733643 DOI: 10.1371/journal.pone.0070772] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/21/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Substituting galactose for glucose in cell culture media has been suggested to enhance mitochondrial metabolism in a variety of cell lines. We studied the effects of carbohydrate availability on growth, differentiation and metabolism of C2C12 myoblasts and myotubes. METHODOLOGY/PRINCIPAL FINDINGS We measured growth rates, ability to differentiate, citrate synthase and respiratory chain activities and several parameters of mitochondrial respiration in C2C12 cells grown in media with varying carbohydrate availability (5 g/l glucose, 1 g/l glucose, 1 g/l galactose, and no added carbohydrates). C2C12 myoblasts grow more slowly without glucose irrespective of the presence of galactose, which is not consumed by the cells, and they fail to differentiate without glucose in the medium. Cells grown in a no-glucose medium (with or without galactose) have lower maximal respiration and spare respiratory capacity than cells grown in the presence of glucose. However, increasing glucose concentration above physiological levels decreases the achievable maximal respiration. C2C12 myotubes differentiated at a high glucose concentration showed higher dependency on oxidative respiration under basal conditions but had lower maximal and spare respiratory capacity when compared to cells differentiated under low glucose condition. Citrate synthase activity or mitochondrial yield were not significantly affected by changes in the available substrate concentration but a trend towards a higher respiratory chain activity was observed at reduced glucose levels. CONCLUSIONS/SIGNIFICANCE Our results show that using galactose to increase oxidative metabolism may not be applicable to every cell line, and the changes in mitochondrial respiratory parameters associated with treating cells with galactose are mainly due to glucose deprivation. Moderate concentrations of glucose (1 g/l) in a growth medium are optimal for mitochondrial respiration in C2C12 cell line while supraphysiological concentrations of glucose cause mitochondrial dysfunction in C2C12 myoblasts and myotubes.
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Affiliation(s)
- Moustafa Elkalaf
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Centre for Research on Diabetes, Metabolism and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michal Anděl
- Centre for Research on Diabetes, Metabolism and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Trnka
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
- Centre for Research on Diabetes, Metabolism and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic
- * E-mail:
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16
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Kosterina YA, Kozenkov II, Kasymov VA, Kamensky PA, Dominova IN, Korolyova YA, Patrusheva VY, Bogachev RS, Litvinova LS, Babak SV, Moiseeva YM, Bogdanov YA, Mukhortova OA, Vavilina YS, Mikhalchenkova TA, Patrushev MV. MITOCHONDRIAL PROTEIN PROFILE AND ITS ROLE IN PATHOLOGIC PROCESSES. BULLETIN OF SIBERIAN MEDICINE 2013. [DOI: 10.20538/1682-0363-2013-3-5-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mitochondria import hundreds of different precursor proteins from the cytosol, and only 13 proteins are encoded by mtDNA itself. Recent investigations demonstrated real size of mitochondrial proteome and complexity of their functions There are many methods using for mitochondrial proteome profiling, that help to understand a molecular mechanisms of mitochondrial functions and identify the causes of disruptions that lead to different disorders. In this review we discuss a recent data in the field of mitochondrial proteomics.
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Affiliation(s)
| | | | - V. A. Kasymov
- Immanuel Kant Baltic Federal University, Kaliningrad
| | | | | | | | | | | | | | - S. V. Babak
- Immanuel Kant Baltic Federal University, Kaliningrad
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17
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Ferreira R, Rocha H, Almeida V, Padrão AI, Santa C, Vilarinho L, Amado F, Vitorino R. Mitochondria proteome profiling: a comparative analysis between gel- and gel-free approaches. Talanta 2013; 115:277-83. [PMID: 24054592 DOI: 10.1016/j.talanta.2013.04.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/29/2013] [Accepted: 04/08/2013] [Indexed: 12/22/2022]
Abstract
Mitochondrial proteomics emerged aiming to disclose the dynamics of mitochondria under various pathophysiological conditions. In the present study we investigated the relative merits of gel-based (2DE and SDS-LC) and gel-free (2D-LC) protein separation approaches and protein identification algorithms (Mascot and Paragon) in the proteome profiling of mitochondria isolated from cultured fibroblasts, a sample traditionally used for diagnosis purposes. Combining data retrieved from 2DE, 2D-LC and SDS-LC and search methods, a total of 696 non-redundant proteins were identified. An overlap of only 19% between the proteins identified by the three different methods was observed when Mascot and Paragon were used. Regarding protein ID, a consistency in the number of identified proteins per sample was noticed for 2DE approach. Independent of the methodological approach chosen, it was noticed that the predominance in mitochondria of hydrophilic proteins with 20-50 kDa and pI 5-6 and 8-9; however, 2D-LC and SDS-LC allowed the enrichment of proteins with a mass below 30 kDa and of basic proteins with pI values above 8. In conclusion, data from the present study highlight the power of integrating different separation technologies and protein identification algorithms.
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Affiliation(s)
- Rita Ferreira
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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18
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Pastila R. Effects of ultraviolet radiation on skin cell proteome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 990:121-7. [PMID: 23378008 DOI: 10.1007/978-94-007-5896-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ultraviolet (UV) radiation is known to cause both positive and negative health effects for humans. The synthesis of vitamin D is one of the rare beneficial effects of UV. The negative effects, such as sunburn and premature photoaging of the skin, increase the risk of skin cancer, which is the most detrimental health consequence of UV radiation. Although proteomics has been extensively applied in various areas of the biomedical field, this technique has not been commonly used in the cutaneous biology. Proteome maps of human keratinocytes and of murine skin have been established to characterize the cutaneous responses and the age-related differences. There are very few publications, in which proteomic techniques have been utilized in photobiology and hence there is no systematic research data available of the UV effects on the skin proteome. The proteomic studies have mainly focused on the UV-induced photoaging, which is the consequence of the long-term chronic UV exposure. Since the use of proteomics has been very narrow in the photobiology, there is room for new studies. Proteomics would offer a cost-effective way to large-scale screen the possible target molecules involved in the UV-derived photodamage, especially what the large-scale effects are after the acute and chronic exposure on the different skin cell populations.
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Affiliation(s)
- Riikka Pastila
- STUK - Radiation and Nuclear Safety Authority, 14, Helsinki, FI-00881, Finland.
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19
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An iTRAQ-based mitoproteomics approach for profiling the nephrotoxicity mechanisms of ochratoxin A in HEK 293 cells. J Proteomics 2013; 78:398-415. [DOI: 10.1016/j.jprot.2012.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/28/2012] [Accepted: 10/11/2012] [Indexed: 01/05/2023]
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20
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Hallahan BP, Daly EM, Simmons A, Moore CJ, Murphy KC, Murphy DDG. Fragile X syndrome: a pilot proton magnetic resonance spectroscopy study in premutation carriers. J Neurodev Disord 2012; 4:23. [PMID: 22958351 PMCID: PMC3443443 DOI: 10.1186/1866-1955-4-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/13/2012] [Indexed: 11/10/2022] Open
Abstract
Purpose There is increasing evidence that neurodevelopmental differences in people with Fragile X syndrome (FraX) may be explained by differences in glutamatergic metabolism. Premutation carriers of FraX were originally considered to be unaffected although several recent reports demonstrate neuroanatomical, cognitive, and emotional differences from controls. However there are few studies on brain metabolism in premutation carriers of FraX. Methods We used proton magnetic resonance spectroscopy to compare neuronal integrity of a number of brain metabolites including N-Acetyl Aspartate, Creatine + Phosphocreatinine, Choline, myoInositol, and Glutamate containing substances (Glx) in 17 male premutation carriers of FraX and 16 male healthy control individuals. Results There was no significant between-group difference in the concentration of any measured brain metabolites. However there was a differential increase in N-acetyl aspartate with aging in premutation FraX individuals compared to controls. Conclusions This is the first 1 H-MRS study to examine premutation FraX individuals. Although we demonstrated no difference in the concentration of any of the metabolites examined between the groups, this may be due to the large age ranges included in the two samples. The differential increase in NAA levels with aging may reflect an abnormal synaptic pruning process.
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Affiliation(s)
- Brian P Hallahan
- Department of Psychiatry, National University of Ireland Galway, Galway, Ireland.
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21
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Stødkilde L, Madsen MG, Palmfeldt J, Topcu SO, Nørregaard R, Olsen LH, Jørgensen TM, Frøkiær J. Urinary proteome analysis in congenital bilateral hydronephrosis. Scand J Urol 2012; 47:43-51. [PMID: 22891811 DOI: 10.3109/00365599.2012.708669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE A proteomics strategy was applied to map protein changes in urine after relief of congenital bilateral hydronephrosis to identify proteins correlated with the pathophysiological processes in congenital obstructive nephropathy as potential urinary biomarkers. MATERIAL AND METHODS Urine samples from 10 infants with bilateral abnormal drainage from the kidneys were collected at the time of relief from obstruction, and after 2 and 4 weeks. Proteomics techniques were used on samples from three patients for identification of protein changes between the three time-points, and enzyme-linked immunosorbent assay (ELISA) was used on samples from all 10 patients for validation of five selected proteins. RESULTS Mass spectrometry quantified 315 protein hits, out of which 33 proteins showed significantly changed urinary excretion between the time-points. Validation by ELISA showed high urinary excretion of fibrinogen, plasminogen, transthyretin and transferrin at the time of relief from obstruction, followed by a significant reduction. In contrast, Tamm-Horsfall protein exhibited the reverse pattern. CONCLUSION Using a mass spectrometry-based proteomics approach, this study identified 33 proteins related to congenital bilateral hydronephrosis, and pinpointed a panel of five proteins consistently linked to this congenital kidney disorder as potential urinary biomarkers.
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Affiliation(s)
- Lene Stødkilde
- The Water and Salt Research Center, Institute of Clinical Medicine, University of Aarhus, Aarhus, Denmark
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22
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Voets AM, Lindsey PJ, Vanherle SJ, Timmer ED, Esseling JJ, Koopman WJH, Willems PHGM, Schoonderwoerd GC, De Groote D, Poll-The BT, de Coo IFM, Smeets HJM. Patient-derived fibroblasts indicate oxidative stress status and may justify antioxidant therapy in OXPHOS disorders. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1971-8. [PMID: 22796146 DOI: 10.1016/j.bbabio.2012.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 06/12/2012] [Accepted: 07/02/2012] [Indexed: 10/28/2022]
Abstract
Oxidative phosphorylation disorders are often associated with increased oxidative stress and antioxidant therapy is frequently given as treatment. However, the role of oxidative stress in oxidative phosphorylation disorders or patients is far from clear and consequently the preventive or therapeutic effect of antioxidants is highly anecdotic. Therefore, we performed a systematic study of a panel of oxidative stress parameters (reactive oxygen species levels, damage and defense) in fibroblasts of twelve well-characterized oxidative phosphorylation patients with a defect in the POLG1 gene, in the mitochondrial DNA-encoded tRNA-Leu gene (m.3243A>G or m.3302A>G) and in one of the mitochondrial DNA-encoded NADH dehydrogenase complex I (CI) subunits. All except two cell lines (one POLG1 and one tRNA-Leu) showed increased reactive oxygen species levels compared with controls, but only four (two CI and two tRNA-Leu) cell lines provided evidence for increased oxidative protein damage. The absence of a correlation between reactive oxygen species levels and oxidative protein damage implies differences in damage prevention or correction. This was investigated by gene expression studies, which showed adaptive and compensating changes involving antioxidants and the unfolded protein response, especially in the POLG1 group. This study indicated that patients display individual responses and that detailed analysis of fibroblasts enables the identification of patients that potentially benefit from antioxidant therapy. Furthermore, the fibroblast model can also be used to search for and test novel, more specific antioxidants or explore ways to stimulate compensatory mechanisms.
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Affiliation(s)
- A M Voets
- Department of Genetics and Cell Biology, Maastricht University, The Netherlands
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23
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Gregersen N, Hansen J, Palmfeldt J. Mitochondrial proteomics--a tool for the study of metabolic disorders. J Inherit Metab Dis 2012; 35:715-26. [PMID: 22526845 DOI: 10.1007/s10545-012-9480-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 12/14/2022]
Abstract
Mitochondria are important for a number of life and death processes, such as energy production, creation of reactive oxygen species, and elicitation of stress responses. These responses range from induction of protein quality control and antioxidant systems to mitochondria elimination and cell death. Mitochondrial dysfunctions are involved in pathologies associated with many diseases, for example metabolic disorders, diabetes, cancers, cardiovascular and neurodegenerative diseases as well as obesity and aging. Mitochondrial proteomics can be a powerful tool in the study of these diseases, especially since it can cover mitochondrial proteins from several metabolic pathways, such as the citric acid cycle, fatty acid oxidation, and respiratory chain, as well as protein networks involved in stress responses. The mitochondrial proteome can consist of more than 1,000 different proteins. However, it is difficult to define the precise number, since mitochondria are dynamic and difficult to purify, and because an unknown number of proteins possess dual or multiple localization, depending on cell type and physiological conditions. This review describes several quantitative studies of proteins from mitochondria isolated by centrifugation, separated by various methods (e.g., electrophoresis and nanoLC), and analyzed by advanced mass spectrometry. We illustrate the methods by showing that multiple pathways and networks are affected in cells from patients carrying gene variations affecting a mitochondrial protein. The study of cultured skin fibroblasts from patients with ethylmalonic aciduria associated with variations in the genes coding for short-chain acyl-CoA dehydrogenase (SCAD) or ETHE1 are two of the examples. The possibility of obtaining mitochondrial proteomics data from whole cell proteomics studies is also exemplified by the involvement of liver mitochondria in metabolic syndrome.
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Affiliation(s)
- Niels Gregersen
- Research Unit for Molecular Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
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24
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Hansen J, Palmfeldt J, Vang S, Corydon TJ, Gregersen N, Bross P. Quantitative proteomics reveals cellular targets of celastrol. PLoS One 2011; 6:e26634. [PMID: 22046318 PMCID: PMC3202559 DOI: 10.1371/journal.pone.0026634] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/30/2011] [Indexed: 12/29/2022] Open
Abstract
Celastrol, a natural substance isolated from plant extracts used in traditional Chinese medicine, has been extensively investigated as a possible drug for treatment of cancer, autoimmune diseases, and protein misfolding disorders. Although studies focusing on celastrol's effects in specific cellular pathways have revealed a considerable number of targets in a diverse array of in vitro models there is an essential need for investigations that can provide a global view of its effects. To assess cellular effects of celastrol and to identify target proteins as biomarkers for monitoring treatment regimes, we performed large-scale quantitative proteomics in cultured human lymphoblastoid cells, a cell type that can be readily prepared from human blood samples. Celastrol substantially modified the proteome composition and 158 of the close to 1800 proteins with robust quantitation showed at least a 1.5 fold change in protein levels. Up-regulated proteins play key roles in cytoprotection with a prominent group involved in quality control and processing of proteins traversing the endoplasmic reticulum. Increased levels of proteins essential for the cellular protection against oxidative stress including heme oxygenase 1, several peroxiredoxins and thioredoxins as well as proteins involved in the control of iron homeostasis were also observed. Specific analysis of the mitochondrial proteome strongly indicated that the mitochondrial association of certain antioxidant defense and apoptosis-regulating proteins increased in cells exposed to celastrol. Analysis of selected mRNA transcripts showed that celastrol activated several different stress response pathways and dose response studies furthermore showed that continuous exposure to sub-micromolar concentrations of celastrol is associated with reduced cellular viability and proliferation. The extensive catalog of regulated proteins presented here identifies numerous cellular effects of celastrol and constitutes a valuable biomarker tool for the development and monitoration of disease treatment strategies.
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Affiliation(s)
- Jakob Hansen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus, Denmark.
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Rocha H, Ferreira R, Carvalho J, Vitorino R, Santa C, Lopes L, Gregersen N, Vilarinho L, Amado F. Characterization of mitochondrial proteome in a severe case of ETF-QO deficiency. J Proteomics 2011; 75:221-8. [PMID: 21596162 DOI: 10.1016/j.jprot.2011.04.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 04/14/2011] [Accepted: 04/28/2011] [Indexed: 01/29/2023]
Abstract
Multiple acyl-CoA dehydrogenase deficiency (MADD) is a mitochondrial fatty acid oxidation disorder caused by mutations that affect electron transfer flavoprotein (ETF) or ETF:ubiquinone oxidoreductase (ETF-QO) or even due to unidentified disturbances of riboflavin metabolism. Besides all the available data on the molecular basis of FAO disorders, including MADD, the pathophysiological mechanisms underlying clinical phenotype development, namely at the mitochondrial level, are poorly understood. In order to contribute to the elucidation of these mechanisms, we isolated mitochondria from cultured fibroblasts, from a patient with a severe MADD presentation due to ETF-QO deficiency, characterize its mitochondrial proteome and compare it with normal controls. The used approach (2-DE-MS/MS) allowed the positive identification of 287 proteins in both patient and controls, presenting 35 of the significant differences in their relative abundance. Among the differentially expressed are proteins associated to binding/folding functions, mitochondrial antioxidant enzymes as well as proteins associated to apoptotic events. The overexpression of chaperones like Hsp60 or mitochondrial Grp75, antioxidant enzymes and apoptotic proteins reflects the mitochondrial response to a complete absence of ETF-QO. Our study provides a global perspective of the mitochondrial proteome plasticity in a severe case of MADD and highlights the main molecular pathways involved in its pathogenesis.
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Affiliation(s)
- H Rocha
- I&D unit, Genetics Department, Medical Genetics Center Jacinto Magalhães of National Institute of Health Ricardo Jorge, Porto, Portugal.
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26
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Broadwater L, Pandit A, Azzam S, Clements R, Vadnal J, Sulak M, Yong VW, Freeman EJ, Gregory RB, McDonough J. Analysis of the mitochondrial proteome in multiple sclerosis cortex. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1812:630-41. [PMID: 21295140 PMCID: PMC3074931 DOI: 10.1016/j.bbadis.2011.01.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 01/09/2011] [Accepted: 01/25/2011] [Indexed: 12/29/2022]
Abstract
Mitochondrial dysfunction has been proposed to play a role in the neuropathology of multiple sclerosis (MS). Previously, we reported significant alterations in the transcription of nuclear-encoded electron transport chain genes in MS and confirmed translational alterations for components of Complexes I and III that resulted in reductions in their activity. To more thoroughly and efficiently elucidate potential alterations in the expression of mitochondrial and related proteins, we have characterized the mitochondrial proteome in postmortem MS and control cortex using Surface-Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS). Using principal component analysis (PCA) and hierarchical clustering techniques we were able to analyze the differential patterns of SELDI-TOF spectra to reveal clusters of peaks which distinguished MS from control samples. Four proteins in particular were responsible for distinguishing disease from control. Peptide fingerprint mapping unambiguously identified these differentially expressed proteins. Three proteins identified are involved in respiration including cytochrome c oxidase subunit 5b (COX5b), the brain specific isozyme of creatine kinase, and hemoglobin β-chain. The fourth protein identified was myelin basic protein (MBP). We then investigated whether these alterations were consistent in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We found that MBP was similarly altered in EAE but the respiratory proteins were not. These data indicate that while the EAE mouse model may mimic aspects of MS neuropathology which result from inflammatory demyelinating events, there is another distinct mechanism involved in mitochondrial dysfunction in gray matter in MS which is not modeled in EAE.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Autopsy
- Biomarkers/analysis
- Blotting, Western
- Brain/metabolism
- Brain/pathology
- Case-Control Studies
- Cerebral Cortex/metabolism
- Cerebral Cortex/pathology
- Disease Models, Animal
- Encephalomyelitis, Autoimmune, Experimental/etiology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Female
- Fluorescent Antibody Technique
- Glycoproteins/administration & dosage
- Humans
- Immunoprecipitation
- Male
- Mice
- Mice, Inbred C57BL
- Middle Aged
- Multiple Sclerosis/metabolism
- Multiple Sclerosis/pathology
- Myelin Basic Protein/metabolism
- Myelin-Oligodendrocyte Glycoprotein
- Peptide Fragments/administration & dosage
- Peptide Mapping
- Principal Component Analysis
- Proteome/analysis
- Proteomics
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Laurie Broadwater
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242
| | - Ashish Pandit
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
| | - Sausan Azzam
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242
| | - Robert Clements
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
| | - Jonathan Vadnal
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
| | - Michael Sulak
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
| | - V. Wee Yong
- Departments of Clinical Neurosciences and Oncology, University of Calgary, Calgary, Alberta, CA T2N 4N1
| | - Ernest J. Freeman
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
| | - Roger B. Gregory
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242
| | - Jennifer McDonough
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242
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Schmidt SP, Corydon TJ, Pedersen CB, Vang S, Palmfeldt J, Stenbroen V, Wanders RJA, Ruiter JPN, Gregersen N. Toxic response caused by a misfolding variant of the mitochondrial protein short-chain acyl-CoA dehydrogenase. J Inherit Metab Dis 2011; 34:465-75. [PMID: 21170680 PMCID: PMC3063561 DOI: 10.1007/s10545-010-9255-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Revised: 11/21/2010] [Accepted: 11/24/2010] [Indexed: 01/19/2023]
Abstract
BACKGROUND Variations in the gene ACADS, encoding the mitochondrial protein short-chain acyl CoA-dehydrogenase (SCAD), have been observed in individuals with clinical symptoms. The phenotype of SCAD deficiency (SCADD) is very heterogeneous, ranging from asymptomatic to severe, without a clear genotype-phenotype correlation, which suggests a multifactorial disorder. The pathophysiological relevance of the genetic variations in the SCAD gene is therefore disputed, and has not yet been elucidated, which is an important step in the investigation of SCADD etiology. AIM To determine whether the disease-associated misfolding variant of SCAD protein, p.Arg107Cys, disturbs mitochondrial function. METHODS We have developed a cell model system, stably expressing either the SCAD wild-type protein or the misfolding SCAD variant protein, p.Arg107Cys (c.319 C > T). The model system was used for investigation of SCAD with respect to expression, degree of misfolding, and enzymatic SCAD activity. Furthermore, cell proliferation and expression of selected stress response genes were investigated as well as proteomic analysis of mitochondria-enriched extracts in order to study the consequences of p.Arg107Cys protein expression using a global approach. CONCLUSIONS We found that expression of the p.Arg107Cys variant SCAD protein gives rise to inactive misfolded protein species, eliciting a mild toxic response manifested though a decreased proliferation rate and oxidative stress, as shown by an increased demand for the mitochondrial antioxidant SOD2. In addition, we found markers of apoptotic activity in the p.Arg107Cys expressing cells, which points to a possible pathophysiological role of this variant protein.
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Affiliation(s)
- Stinne P Schmidt
- Research Unit for Molecular Medicine, Aarhus University Hospital, Skejby, Denmark.
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28
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Palmfeldt J, Vang S, Stenbroen V, Pavlou E, Baycheva M, Buchal G, Monavari AA, Augoustides-Savvopoulou P, Mandel H, Gregersen N. Proteomics reveals that redox regulation is disrupted in patients with ethylmalonic encephalopathy. J Proteome Res 2011; 10:2389-96. [PMID: 21410200 DOI: 10.1021/pr101218d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and revealed seven differentially regulated proteins compared with healthy controls. Two proteins involved in pathways of detoxification and oxidative/reductive stress were underrepresented in EE patient samples: mitochondrial superoxide dismutase (SOD2) and aldehyde dehydrogenase X (ALDH1B). Sulfide:quinone oxidoreductase (SQRDL), which takes part in the same sulfide pathway as ETHE1, was also underrepresented in EE patients. The other differentially regulated proteins were apoptosis inducing factor (AIFM1), lactate dehydrogenase (LDHB), chloride intracellular channel (CLIC4) and dimethylarginine dimethylaminohydrolase 1 (DDAH1). These proteins have been reported to be involved in encephalopathy, energy metabolism, ion transport, and nitric oxide regulation, respectively. Interestingly, oxidoreductase activity was overrepresented among the regulated proteins indicating that redox perturbation plays an important role in the molecular mechanism of EE. This observation may explain the wide range of symptoms associated with the disease, and highlights the potency of the novel gaseous mediator sulfide.
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Affiliation(s)
- Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University Hospital, Skejby, Denmark.
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29
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Gianazza E, Eberini I, Sensi C, Barile M, Vergani L, Vanoni MA. Energy matters: mitochondrial proteomics for biomedicine. Proteomics 2011; 11:657-74. [PMID: 21241019 DOI: 10.1002/pmic.201000412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/22/2010] [Accepted: 11/03/2010] [Indexed: 12/16/2022]
Abstract
This review compiles results of medical relevance from mitochondrial proteomics, grouped either according to the type of disease - genetic or degenerative - or to the involved mechanism - oxidative stress or apoptosis. The findings are commented in the light of our current understanding of uniformity/variability in cell responses to different stimuli. Specificities in the conceptual and technical approaches to human mitochondrial proteomics are also outlined.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, Milano, Italy.
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30
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Addis MF, Cappuccinelli R, Tedde V, Pagnozzi D, Viale I, Meloni M, Salati F, Roggio T, Uzzau S. Influence of Moraxella sp. colonization on the kidney proteome of farmed gilthead sea breams (Sparus aurata, L.). Proteome Sci 2010; 8:50. [PMID: 20939867 PMCID: PMC2964643 DOI: 10.1186/1477-5956-8-50] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 10/12/2010] [Indexed: 12/02/2022] Open
Abstract
Background Currently, presence of Moraxella sp. in internal organs of fish is not considered detrimental for fish farming. However, bacterial colonization of internal organs can affect fish wellness and decrease growth rate, stress resistance, and immune response. Recently, there have been reports by farmers concerning slow growth, poor feed conversion, and low average weight increase of fish farmed in offshore floating sea cages, often associated with internal organ colonization by Moraxella sp. Therefore, presence of these opportunistic bacteria deserves further investigations for elucidating incidence and impact on fish metabolism. Results A total of 960 gilthead sea breams (Sparus aurata, L.), collected along 17 months from four offshore sea cage plants and two natural lagoons in Sardinia, were subjected to routine microbiological examination of internal organs throughout the production cycle. Thirteen subjects (1.35%) were found positive for Moraxella sp. in the kidney (7), brain (3), eye (1), spleen (1), and perivisceral fat (1). In order to investigate the influence of Moraxella sp. colonization, positive and negative kidney samples were subjected to a differential proteomics study by means of 2-D PAGE and mass spectrometry. Interestingly, Moraxella sp. infected kidneys displayed a concerted upregulation of several mitochondrial enzymes compared to negative tissues, reinforcing previous observations following lipopolysaccharide (LPS) challenge in fish. Conclusions Presence of Moraxella sp. in farmed sea bream kidney is able to induce proteome alterations similar to those described following LPS challenge in other fish species. This study revealed that Moraxella sp. might be causing metabolic alterations in fish, and provided indications on proteins that could be investigated as markers of infection by Gram-negative bacteria within farming plants.
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Abstract
For nearly three decades, the sequence of the human mitochondrial genome (mtDNA) has provided a molecular framework for understanding maternally inherited diseases. However, the vast majority of human mitochondrial disorders are caused by nuclear genome defects, which is not surprising since the mtDNA encodes only 13 proteins. Advances in genomics, mass spectrometry, and computation have only recently made it possible to systematically identify the complement of over 1,000 proteins that comprise the mammalian mitochondrial proteome. Here, we review recent progress in characterizing the mitochondrial proteome and highlight insights into its complexity, tissue heterogeneity, evolutionary origins, and biochemical versatility. We then discuss how this proteome is being used to discover the genetic basis of respiratory chain disorders as well as to expand our definition of mitochondrial disease. Finally, we explore future prospects and challenges for using the mitochondrial proteome as a foundation for systems analysis of the organelle.
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Affiliation(s)
- Sarah E Calvo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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32
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Pedersen CB, Zolkipli Z, Vang S, Palmfeldt J, Kjeldsen M, Stenbroen V, Schmidt SP, Wanders RJA, Ruiter JPN, Wibrand F, Tein I, Gregersen N. Antioxidant dysfunction: potential risk for neurotoxicity in ethylmalonic aciduria. J Inherit Metab Dis 2010; 33:211-22. [PMID: 20443061 DOI: 10.1007/s10545-010-9086-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 03/08/2010] [Accepted: 03/10/2010] [Indexed: 11/29/2022]
Abstract
Mitochondrial dysfunction and oxidative stress are central to the molecular basis of several human diseases associated with neuromuscular disabilities. We hypothesize that mitochondrial dysfunction also contributes to the neuromuscular symptoms observed in patients with ethylmalonic aciduria and homozygosity for ACADS c.625G>A-a common variant of the short-chain acyl-coenzyme A (CoA) dehydrogenase (SCAD) enzyme in the mitochondrial fatty acid oxidation pathway. This study sought to identify the specific factors that initiate cell dysfunction in these patients. We investigated fibroblast cultures from 10 patients with neuromuscular disabilities, elevated levels of ethylmalonic acid (EMA) (>50 mmol/mol creatinine), and ACADS c.625G>A homozygosity. Functional analyses, i.e., ACADS gene and protein expression as well as SCAD enzyme activity measurements, were performed together with a global nano liquid chromatography tandem mass spectroscopy (nano-LC-MS/MS)-based screening of the mitochondrial proteome in patient fibroblasts. Moreover, cell viability of patient fibroblasts exposed to menadione-induced oxidative stress was evaluated. Loss of SCAD function was detected in the patient group, most likely due to decreased ACADS gene expression and/or elimination of misfolded SCAD protein. Analysis of the mitochondrial proteome in patient fibroblasts identified a number of differentially expressed protein candidates, including reduced expression of the antioxidant superoxide dismutase 2 (SOD2). Additionally, patient fibroblasts demonstrated significantly higher sensitivity to oxidative stress than control fibroblasts. We propose that reduced mitochondrial antioxidant capacity is a potential risk factor for ACADS c.625G>A-associated ethylmalonic aciduria and that mitochondrial dysfunction contributes to the neurotoxicity observed in patients.
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Affiliation(s)
- Christina B Pedersen
- Research Unit for Molecular Medicine, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, Aarhus N, Denmark.
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33
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David JP, Coissac E, Melodelima C, Poupardin R, Riaz MA, Chandor-Proust A, Reynaud S. Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics 2010; 11:216. [PMID: 20356352 PMCID: PMC2867825 DOI: 10.1186/1471-2164-11-216] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 03/31/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, mosquito control programs are now threatened by the emergence of insecticide resistance. Hitherto, most research efforts have been focused on elucidating the molecular basis of inherited resistance. Less attention has been paid to the short-term response of mosquitoes to insecticides and pollutants which could have a significant impact on insecticide efficacy. Here, a combination of LongSAGE and Solexa sequencing was used to perform a deep transcriptome analysis of larvae of the dengue vector Aedes aegypti exposed for 48 h to sub-lethal doses of three chemical insecticides and three anthropogenic pollutants. RESULTS Thirty millions 20 bp cDNA tags were sequenced, mapped to the mosquito genome and clustered, representing 6850 known genes and 4868 additional clusters not located within predicted genes. Mosquitoes exposed to insecticides or anthropogenic pollutants showed considerable modifications of their transcriptome. Genes encoding cuticular proteins, transporters, and enzymes involved in the mitochondrial respiratory chain and detoxification processes were particularly affected. Genes and molecular mechanisms potentially involved in xenobiotic response and insecticide tolerance were identified. CONCLUSIONS The method used in the present study appears as a powerful approach for investigating fine transcriptome variations in genome-sequenced organisms and can provide useful informations for the detection of novel transcripts. At the biological level, despite low concentrations and no apparent phenotypic effects, the significant impact of these xenobiotics on mosquito transcriptomes raise important questions about the 'hidden impact' of anthropogenic pollutants on ecosystems and consequences on vector control.
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Affiliation(s)
- Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA, UMR 5553 CNRS - Université Grenoble), France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA, UMR 5553 CNRS - Université Grenoble), France
| | | | - Rodolphe Poupardin
- Laboratoire d'Ecologie Alpine (LECA, UMR 5553 CNRS - Université Grenoble), France
| | - Muhammad Asam Riaz
- Laboratoire d'Ecologie Alpine (LECA, UMR 5553 CNRS - Université Grenoble), France
| | | | - Stéphane Reynaud
- Laboratoire d'Ecologie Alpine (LECA, UMR 5553 CNRS - Université Grenoble), France
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Baiges I, Palmfeldt J, Bladé C, Gregersen N, Arola L. Lipogenesis is decreased by grape seed proanthocyanidins according to liver proteomics of rats fed a high fat diet. Mol Cell Proteomics 2010; 9:1499-513. [PMID: 20332082 DOI: 10.1074/mcp.m000055-mcp201] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bioactive proanthocyanidins have been reported to have several beneficial effects on health in relation to metabolic syndrome, type 2 diabetes, and cardiovascular disease. We studied the effect of grape seed proanthocyanidin extract (GSPE) in rats fed a high fat diet (HFD). This is the first study of the effects of flavonoids on the liver proteome of rats suffering from metabolic syndrome. Three groups of rats were fed over a period of 13 weeks either a chow diet (control), an HFD, or a high fat diet supplemented for the last 10 days with GSPE (HFD + GSPE). The liver proteome was fractionated, using a Triton X-114-based two-phase separation, into soluble and membrane protein fractions so that total proteome coverage was considerably improved. The data from isobaric tag for relative and absolute quantitation (iTRAQ)-based nano-LC-MS/MS analysis revealed 90 proteins with a significant (p < 0.05) minimal expression difference of 20% due to metabolic syndrome (HFD versus control) and 75 proteins due to GSPE treatment (HFD + GSPE versus HFD). The same animals have previously been studied (Quesada, H., del Bas, J. M., Pajuelo, D., Díaz, S., Fernandez-Larrea, J., Pinent, M., Arola, L., Salvadó, M. J., and Bladé, C. (2009) Grape seed proanthocyanidins correct dyslipidemia associated with a high-fat diet in rats and repress genes controlling lipogenesis and VLDL assembling in liver. Int. J. Obes. 33, 1007-1012), and GSPE was shown to correct dyslipidemia observed in HFD-fed rats probably through the repression of hepatic lipogenesis. Our data corroborate those findings with an extensive list of proteins describing the induction of hepatic glycogenesis, glycolysis, and fatty acid and triglyceride synthesis in HFD, whereas the opposite pattern was observed to a large extent in GSPE-treated animals. GSPE was shown to have a wider effect than previously thought, and putative targets of GSPE involved in the reversal of the symptoms of metabolic syndrome were revealed. Some of these novel candidate proteins such as GFPT1, CD36, PLAA (phospholipase A(2)-activating protein), METTL7B, SLC30A1, several G signaling proteins, and the sulfide-metabolizing ETHE1 and SQRDL (sulfide-quinone reductase-like) might be considered as drug targets for the treatment of metabolic syndrome.
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Affiliation(s)
- Isabel Baiges
- Biochemistry and Biotechnology Department, Universitat Rovira i Virgili, 43007 Tarragona, Spain.
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