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Pegoraro C, Domingo-Ortí I, Conejos-Sánchez I, Vicent MJ. Unlocking the Mitochondria for Nanomedicine-based Treatments: Overcoming Biological Barriers, Improving Designs, and Selecting Verification Techniques. Adv Drug Deliv Rev 2024; 207:115195. [PMID: 38325562 DOI: 10.1016/j.addr.2024.115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Enhanced targeting approaches will support the treatment of diseases associated with dysfunctional mitochondria, which play critical roles in energy generation and cell survival. Obstacles to mitochondria-specific targeting include the presence of distinct biological barriers and the need to pass through (or avoid) various cell internalization mechanisms. A range of studies have reported the design of mitochondrially-targeted nanomedicines that navigate the complex routes required to influence mitochondrial function; nonetheless, a significant journey lies ahead before mitochondrially-targeted nanomedicines become suitable for clinical use. Moving swiftly forward will require safety studies, in vivo assays confirming effectiveness, and methodologies to validate mitochondria-targeted nanomedicines' subcellular location/activity. From a nanomedicine standpoint, we describe the biological routes involved (from administration to arrival within the mitochondria), the features influencing rational design, and the techniques used to identify/validate successful targeting. Overall, rationally-designed mitochondria-targeted-based nanomedicines hold great promise for precise subcellular therapeutic delivery.
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Affiliation(s)
- Camilla Pegoraro
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inés Domingo-Ortí
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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2
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Hansen FM, Kremer LS, Karayel O, Bludau I, Larsson NG, Kühl I, Mann M. Mitochondrial phosphoproteomes are functionally specialized across tissues. Life Sci Alliance 2024; 7:e202302147. [PMID: 37984987 PMCID: PMC10662294 DOI: 10.26508/lsa.202302147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Mitochondria are essential organelles whose dysfunction causes human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondrial fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Increasing evidence suggests that phosphorylation may play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. Building on recent advances in mass spectrometry (MS)-based proteomics, we here quantitatively profile mitochondrial tissue proteomes along with their matching phosphoproteomes. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and performed high-resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue-specific mitochondrial proteins (mitophos.de). Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on dynamin-related protein 1 responsible for its mitochondrial recruitment and fission initiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.
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Affiliation(s)
- Fynn M Hansen
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laura S Kremer
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ozge Karayel
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Isabell Bludau
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nils-Göran Larsson
- https://ror.org/056d84691 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell, UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthias Mann
- https://ror.org/04py35477 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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3
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Sarmento MJ, Llorente A, Petan T, Khnykin D, Popa I, Nikolac Perkovic M, Konjevod M, Jaganjac M. The expanding organelle lipidomes: current knowledge and challenges. Cell Mol Life Sci 2023; 80:237. [PMID: 37530856 PMCID: PMC10397142 DOI: 10.1007/s00018-023-04889-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lipids in cell membranes and subcellular compartments play essential roles in numerous cellular processes, such as energy production, cell signaling and inflammation. A specific organelle lipidome is characterized by lipid synthesis and metabolism, intracellular trafficking, and lipid homeostasis in the organelle. Over the years, considerable effort has been directed to the identification of the lipid fingerprints of cellular organelles. However, these fingerprints are not fully characterized due to the large variety and structural complexity of lipids and the great variability in the abundance of different lipid species. The process becomes even more challenging when considering that the lipidome differs in health and disease contexts. This review summarizes the information available on the lipid composition of mammalian cell organelles, particularly the lipidome of the nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus, plasma membrane and organelles in the endocytic pathway. The lipid compositions of extracellular vesicles and lamellar bodies are also described. In addition, several examples of subcellular lipidome dynamics under physiological and pathological conditions are presented. Finally, challenges in mapping organelle lipidomes are discussed.
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Affiliation(s)
- Maria J Sarmento
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167, Oslo, Norway
- Faculty of Medicine, Centre for Cancer Cell Reprogramming, University of Oslo, Montebello, 0379, Oslo, Norway
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Iuliana Popa
- Pharmacy Department, Bâtiment Henri Moissan, University Paris-Saclay, 17 Avenue des Sciences, 91400, Orsay, France
| | | | - Marcela Konjevod
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Morana Jaganjac
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia.
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4
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Schäfer JA, Sutandy FXR, Münch C. Omics-based approaches for the systematic profiling of mitochondrial biology. Mol Cell 2023; 83:911-926. [PMID: 36931258 DOI: 10.1016/j.molcel.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.
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Affiliation(s)
- Jasmin Adriana Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - F X Reymond Sutandy
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany.
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5
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Jauregui AM, Cubero Cortés ZM, Meehan SD, Bhattacharya SK. Isolation of Mitochondrial Lipids and Mass Spectrometric Analysis. Methods Mol Biol 2023; 2625:1-6. [PMID: 36653628 DOI: 10.1007/978-1-0716-2966-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mitochondria participate in many important metabolic processes in the body. The lipid profile of mitochondria is especially important in membrane regulation and pathway signaling. The isolation and study of these lipids can provide unparalleled information about the mechanisms behind these cellular processes. In this chapter, we describe a protocol to isolate mitochondrial lipids from homogenized murine optic nerves. The lipid extraction was performed using butanol-methanol (BUME) and subsequently analyzed using liquid chromatography-mass spectrometry. Further analysis of the raw data was conducted using LipidSearch™ and MetaboAnalyst 4.0.
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Affiliation(s)
- Alexa M Jauregui
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA
- Miami Integrative Metabolomics Research Center, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sean D Meehan
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA
- Miami Integrative Metabolomics Research Center, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA.
- Miami Integrative Metabolomics Research Center, Miami, FL, USA.
- University of Miami Miller School of Medicine, Miami, FL, USA.
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6
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Mishra K, Péter M, Nardiello AM, Keller G, Llado V, Fernandez-Garcia P, Kahlert UD, Barasch D, Saada A, Török Z, Balogh G, Escriba PV, Piotto S, Kakhlon O. Multifaceted Analyses of Isolated Mitochondria Establish the Anticancer Drug 2-Hydroxyoleic Acid as an Inhibitor of Substrate Oxidation and an Activator of Complex IV-Dependent State 3 Respiration. Cells 2022; 11:cells11030578. [PMID: 35159387 PMCID: PMC8834245 DOI: 10.3390/cells11030578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 02/04/2023] Open
Abstract
The synthetic fatty acid 2-hydroxyoleic acid (2OHOA) has been extensively investigated as a cancer therapy mainly based on its regulation of membrane lipid composition and structure, activating various cell fate pathways. We discovered, additionally, that 2OHOA can uncouple oxidative phosphorylation, but this has never been demonstrated mechanistically. Here, we explored the effect of 2OHOA on mitochondria isolated by ultracentrifugation from U118MG glioblastoma cells. Mitochondria were analyzed by shotgun lipidomics, molecular dynamic simulations, spectrophotometric assays for determining respiratory complex activity, mass spectrometry for assessing beta oxidation and Seahorse technology for bioenergetic profiling. We showed that the main impact of 2OHOA on mitochondrial lipids is their hydroxylation, demonstrated by simulations to decrease co-enzyme Q diffusion in the liquid disordered membranes embedding respiratory complexes. This decreased co-enzyme Q diffusion can explain the inhibition of disjointly measured complexes I–III activity. However, it doesn’t explain how 2OHOA increases complex IV and state 3 respiration in intact mitochondria. This increased respiration probably allows mitochondrial oxidative phosphorylation to maintain ATP production against the 2OHOA-mediated inhibition of glycolytic ATP production. This work correlates 2OHOA function with its modulation of mitochondrial lipid composition, reflecting both 2OHOA anticancer activity and adaptation to it by enhancement of state 3 respiration.
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Affiliation(s)
- Kumudesh Mishra
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 9112102, Israel;
- Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel; (G.K.); (D.B.); (A.S.)
| | - Mária Péter
- Lipodom Ltd., Dorottya Utca 35-37, 6726 Szeged, Hungary; (M.P.); (Z.T.); (G.B.)
- Biological Research Centre, Institute of Biochemistry, 6726 Szeged, Hungary
| | - Anna Maria Nardiello
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy;
- Bionam Center for Biomaterials, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy
| | - Guy Keller
- Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel; (G.K.); (D.B.); (A.S.)
- Department of Genetics, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 9112102, Israel
| | - Victoria Llado
- Laminar Pharmaceuticals, Ctra. de Valldemossa Km. 7, 4 Parc BIT Ed. Naorte Bolque A-1°-3, 07121 Palma de Mallorca, Spain; (V.L.); (P.F.-G.)
| | - Paula Fernandez-Garcia
- Laminar Pharmaceuticals, Ctra. de Valldemossa Km. 7, 4 Parc BIT Ed. Naorte Bolque A-1°-3, 07121 Palma de Mallorca, Spain; (V.L.); (P.F.-G.)
| | - Ulf D. Kahlert
- Molecular and Experimental Surgery, Clinic for General, Visceral, Vascular, and Transplant Surgery, Medical Faculty, University Hospital Magdeburg, 39120 Magdeburg, Germany;
| | - Dinorah Barasch
- Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel; (G.K.); (D.B.); (A.S.)
- Mass Spectrometry Unit, Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ann Saada
- Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel; (G.K.); (D.B.); (A.S.)
- Department of Genetics, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 9112102, Israel
| | - Zsolt Török
- Lipodom Ltd., Dorottya Utca 35-37, 6726 Szeged, Hungary; (M.P.); (Z.T.); (G.B.)
- Biological Research Centre, Institute of Biochemistry, 6726 Szeged, Hungary
| | - Gábor Balogh
- Lipodom Ltd., Dorottya Utca 35-37, 6726 Szeged, Hungary; (M.P.); (Z.T.); (G.B.)
- Biological Research Centre, Institute of Biochemistry, 6726 Szeged, Hungary
| | - Pablo V. Escriba
- Laminar Pharmaceuticals, Ctra. de Valldemossa Km. 7, 4 Parc BIT Ed. Naorte Bolque A-1°-3, 07121 Palma de Mallorca, Spain; (V.L.); (P.F.-G.)
- Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Correspondence: (P.V.E.); (S.P.); (O.K.)
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy;
- Bionam Center for Biomaterials, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy
- Correspondence: (P.V.E.); (S.P.); (O.K.)
| | - Or Kakhlon
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem 9112102, Israel;
- Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel; (G.K.); (D.B.); (A.S.)
- Correspondence: (P.V.E.); (S.P.); (O.K.)
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7
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Ayer A, Fazakerley DJ, James DE, Stocker R. The role of mitochondrial reactive oxygen species in insulin resistance. Free Radic Biol Med 2022; 179:339-362. [PMID: 34775001 DOI: 10.1016/j.freeradbiomed.2021.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/31/2021] [Accepted: 11/06/2021] [Indexed: 12/21/2022]
Abstract
Insulin resistance is one of the earliest pathological features of a suite of diseases including type 2 diabetes collectively referred to as metabolic syndrome. There is a growing body of evidence from both pre-clinical studies and human cohorts indicating that reactive oxygen species, such as the superoxide radical anion and hydrogen peroxide are key players in the development of insulin resistance. Here we review the evidence linking mitochondrial reactive oxygen species generated within mitochondria with insulin resistance in adipose tissue and skeletal muscle, two major insulin sensitive tissues. We outline the relevant mitochondria-derived reactive species, how the mitochondrial redox state is regulated, and methodologies available to measure mitochondrial reactive oxygen species. Importantly, we highlight key experimental issues to be considered when studying the role of mitochondrial reactive oxygen species in insulin resistance. Evaluating the available literature on both mitochondrial reactive oxygen species/redox state and insulin resistance in a variety of biological systems, we conclude that the weight of evidence suggests a likely role for mitochondrial reactive oxygen species in the etiology of insulin resistance in adipose tissue and skeletal muscle. However, major limitations in the methods used to study reactive oxygen species in insulin resistance as well as the lack of data linking mitochondrial reactive oxygen species and cytosolic insulin signaling pathways are significant obstacles in proving the mechanistic link between these two processes. We provide a framework to guide future studies to provide stronger mechanistic information on the link between mitochondrial reactive oxygen species and insulin resistance as understanding the source, localization, nature, and quantity of mitochondrial reactive oxygen species, their targets and downstream signaling pathways may pave the way for important new therapeutic strategies.
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Affiliation(s)
- Anita Ayer
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Daniel J Fazakerley
- Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - David E James
- Charles Perkins Centre, Sydney Medical School, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Roland Stocker
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.
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8
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Hoene M, Kappler L, Kollipara L, Hu C, Irmler M, Bleher D, Hoffmann C, Beckers J, Hrabě de Angelis M, Häring HU, Birkenfeld AL, Peter A, Sickmann A, Xu G, Lehmann R, Weigert C. Exercise prevents fatty liver by modifying the compensatory response of mitochondrial metabolism to excess substrate availability. Mol Metab 2021; 54:101359. [PMID: 34695608 PMCID: PMC8671118 DOI: 10.1016/j.molmet.2021.101359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 02/06/2023] Open
Abstract
Objective Liver mitochondria adapt to high-calorie intake. We investigated how exercise alters the early compensatory response of mitochondria, thus preventing fatty liver disease as a long-term consequence of overnutrition. Methods We compared the effects of a steatogenic high-energy diet (HED) for six weeks on mitochondrial metabolism of sedentary and treadmill-trained C57BL/6N mice. We applied multi-OMICs analyses to study the alterations in the proteome, transcriptome, and lipids in isolated mitochondria of liver and skeletal muscle as well as in whole tissue and examined the functional consequences by high-resolution respirometry. Results HED increased the respiratory capacity of isolated liver mitochondria, both in sedentary and in trained mice. However, proteomics analysis of the mitochondria and transcriptomics indicated that training modified the adaptation of the hepatic metabolism to HED on the level of respiratory complex I, glucose oxidation, pyruvate and acetyl-CoA metabolism, and lipogenesis. Training also counteracted the HED-induced glucose intolerance, the increase in fasting insulin, and in liver fat by lowering diacylglycerol species and c-Jun N-terminal kinase (JNK) phosphorylation in the livers of trained HED-fed mice, two mechanisms that can reverse hepatic insulin resistance. In skeletal muscle, the combination of HED and training improved the oxidative capacity to a greater extent than training alone by increasing respiration of isolated mitochondria and total mitochondrial protein content. Conclusion We provide a comprehensive insight into the early adaptations of mitochondria in the liver and skeletal muscle to HED and endurance training. Our results suggest that exercise disconnects the HED-induced increase in mitochondrial substrate oxidation from pyruvate and acetyl-CoA-driven lipid synthesis. This could contribute to the prevention of deleterious long-term effects of high fat and sugar intake on hepatic mitochondrial function and insulin sensitivity. High-energy diet promotes mitochondrial respiration in liver independent of training. High-energy diet combined with training disconnects substrate oxidation from lipid synthesis. High-energy diet combined with training reduces complex I formation in the liver. Trained skeletal muscle unburdens the liver from substrate overload. Comprehensive resource of mitochondrial adaptations to high-energy diet and training.
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Affiliation(s)
- Miriam Hoene
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Lisa Kappler
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Martin Irmler
- Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
| | - Daniel Bleher
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Christoph Hoffmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Johannes Beckers
- Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany; Technische Universität München, Chair of Experimental Genetics, 85354, Freising, Germany; German Center for Diabetes Research (DZD), Germany
| | - Martin Hrabě de Angelis
- Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany; Technische Universität München, Chair of Experimental Genetics, 85354, Freising, Germany; German Center for Diabetes Research (DZD), Germany
| | - Hans-Ulrich Häring
- German Center for Diabetes Research (DZD), Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
| | - Andreas L Birkenfeld
- German Center for Diabetes Research (DZD), Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany; Department of Internal Medicine IV, University Hospital Tuebingen, Tuebingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
| | - Cora Weigert
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany.
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9
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Niba ETE, Awano H, Lee T, Takeshima Y, Shinohara M, Nishio H, Matsuo M. Dystrophin Dp71 Subisoforms Localize to the Mitochondria of Human Cells. Life (Basel) 2021; 11:life11090978. [PMID: 34575126 PMCID: PMC8468555 DOI: 10.3390/life11090978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by deficiency in dystrophin, a protein product encoded by the DMD gene. Mitochondrial dysfunction is now attracting much attention as a central player in DMD pathology. However, dystrophin has never been explored in human mitochondria. Here, we analyzed dystrophin in cDNAs and mitochondrial fractions of human cells. Mitochondrial fraction was obtained using a magnetic-associated cell sorting (MACS) technology. Dystrophin was analyzed by reverse transcription (RT)-PCR and western blotting using an antibody against the dystrophin C-terminal. In isolated mitochondrial fraction from HEK293 cells, dystrophin was revealed as a band corresponding to Dp71b and Dp71ab subisoforms. Additionally, in mitochondria from HeLa, SH-SY5Y, CCL-136 and HepG2 cells, signals for Dp71b and Dp71ab were revealed as well. Concomitantly, dystrophin mRNAs encoding Dp71b and Dp71ab were disclosed by RT-PCR in these cells. Primary cultured myocytes from three dystrophinopathy patients showed various levels of mitochondrial Dp71 expression. Coherently, levels of mRNA were different in all cells reflecting the protein content, which indicated predominant accumulation of Dp71. Dystrophin was demonstrated to be localized to human mitochondrial fraction, specifically as Dp71 subisoforms. Myocytes derived from dystrophinopathy patients manifested different levels of mitochondrial Dp71, with higher expression revealed in myocytes from Becker muscular dystrophy (BMD) patient-derived myocytes.
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Affiliation(s)
- Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
- Correspondence: ; Tel.: +81-78-382-5543
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 663-8501, Japan; (T.L.); (Y.T.)
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 663-8501, Japan; (T.L.); (Y.T.)
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Hisahide Nishio
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan;
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan;
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10
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Chang M, Wang Q, Liu X, Shi X, Xu G. Facile Synthesis of Antibody-Coupled Polydopamine-Coated Magnetic Graphene Oxide Composites for Efficient Immunopurification and Metabolomics Analysis of Mitochondria. Anal Chem 2021; 93:11099-11107. [PMID: 34347447 DOI: 10.1021/acs.analchem.1c01101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As a vital hub, a mitochondrion houses metabolic pathways that play important roles in cellular physiology. Aberrant metabolites occurring in mitochondria are closely associated with the emergence and progression of various mitochondria-related diseases. Therefore, a simple and versatile approach to efficiently purify intact mitochondria is urgently needed to precisely and comprehensively characterize the composition and abundance of the mitochondrial metabolome in different physiological and pathological states. In this work, novel immunoaffinitive magnetic composites MagG@PD@Avidin@TOM20 were prepared to achieve highly selective isolation of intact mitochondria from three different hepatocytes (LO2, HepG2, and Huh7). The prepared composites inherit combined merits, including strong magnetic responsiveness, excellent stability, and specific and high affinity between antibody TOM20 and mitochondrial outer membrane protein. These mitochondria attached on MagG@PD@Avidin@TOM20 were characterized by the western blot and fluorescence microscopy to confirm their purity and integrity, which are vital for reliable mitochondrial metabolic analysis. Subsequently, ultrahigh-performance liquid chromatography-high-resolution mass spectrometry-based untargeted metabolomics analysis was conducted to characterize the metabolomes in the immunopurified mitochondria and whole cells. Notably, the metabolite profiles of whole cells and mitochondria including itaconic acid, acetylcarnitine, malic acid, etc., were significantly different. These data underscore the importance of determining metabolites at the mitochondrial level, which would supplement us new knowledge at the subcellular level.
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Affiliation(s)
- Mengmeng Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Sheridan E, Vercellino S, Cursi L, Adumeau L, Behan JA, Dawson KA. Understanding intracellular nanoparticle trafficking fates through spatiotemporally resolved magnetic nanoparticle recovery. NANOSCALE ADVANCES 2021; 3:2397-2410. [PMID: 36134166 PMCID: PMC9419038 DOI: 10.1039/d0na01035a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/21/2021] [Indexed: 05/08/2023]
Abstract
The field of nanomedicine has the potential to be a game-changer in global health, with possible applications in prevention, diagnostics, and therapeutics. However, despite extensive research focus and funding, the forecasted explosion of novel nanomedicines is yet to materialize. We believe that clinical translation is ultimately hampered by a lack of understanding of how nanoparticles really interact with biological systems. When placed in a biological environment, nanoparticles adsorb a biomolecular layer that defines their biological identity. The challenge for bionanoscience is therefore to understand the evolution of the interactions of the nanoparticle-biomolecules complex as the nanoparticle is trafficked through the intracellular environment. However, to progress on this route, scientists face major challenges associated with isolation of specific intracellular compartments for analysis, complicated by the diversity of trafficking events happening simultaneously and the lack of synchronization between individual events. In this perspective article, we reflect on how magnetic nanoparticles can help to tackle some of these challenges as part of an overall workflow and act as a useful platform to investigate the bionano interactions within the cell that contribute to this nanoscale decision making. We discuss both established and emerging techniques for the magnetic extraction of nanoparticles and how they can potentially be used as tools to study the intracellular journey of nanomaterials inside the cell, and their potential to probe nanoscale decision-making events. We outline the inherent limitations of these techniques when investigating particular bio-nano interactions along with proposed strategies to improve both specificity and resolution. We conclude by describing how the integration of magnetic nanoparticle recovery with sophisticated analysis at the single-particle level could be applied to resolve key questions for this field in the future.
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Affiliation(s)
- Emily Sheridan
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Silvia Vercellino
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Biomolecular and Biomedical Science, University College Dublin Belfield Dublin 4 Ireland
| | - Lorenzo Cursi
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Laurent Adumeau
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - James A Behan
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, University College Dublin Belfield Dublin 4 Ireland
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12
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Aoki T, Okuma Y, Becker LB, Hayashida K, Shinozaki K. Methodological Issue of Mitochondrial Isolation in Acute-Injury Rat Model: Asphyxia Cardiac Arrest and Resuscitation. Front Med (Lausanne) 2021; 8:666735. [PMID: 33912580 PMCID: PMC8071985 DOI: 10.3389/fmed.2021.666735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Background: Identification of the mechanisms underlying mitochondrial dysfunction is key to understanding the pathophysiology of acute injuries such as cardiac arrest (CA); however, effective methods for measurement of mitochondrial function associated with mitochondrial isolation have been debated for a long time. This study aimed to evaluate the dysregulation of mitochondrial respiratory function after CA while testing the sampling bias that might be induced by the mitochondrial isolation method. Materials and Methods: Adult rats were subjected to 10-min asphyxia-induced CA. 30 min after resuscitation, the brain and kidney mitochondria from animals in sham and CA groups were isolated (n = 8, each). The mitochondrial quantity, expressed as protein concentration (isolation yields), was determined, and the oxygen consumption rates were measured. ADP-dependent (state-3) and ADP-limited (state-4) respiration activities were compared between the groups. Mitochondrial quantity was evaluated based on citrate synthase (CS) activity and cytochrome c concentration, measured independent of the isolation yields. Results: The state-3 respiration activity and isolation yield in the CA group were significantly lower than those in the sham group (brain, p < 0.01; kidney, p < 0.001). The CS activity was significantly lower in the CA group as compared to that in the sham group (brain, p < 0.01; kidney, p < 0.01). Cytochrome c levels in the CA group showed a similar trend (brain, p = 0.08; kidney, p = 0.25). Conclusions: CA decreased mitochondrial respiration activity and the quantity of mitochondria isolated from the tissues. Owing to the nature of fragmented or damaged mitochondrial membranes caused by acute injury, there is a potential loss of disrupted mitochondria. Thus, it is plausible that the mitochondrial function in the acute-injury model may be underestimated as this loss is not considered.
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Affiliation(s)
- Tomoaki Aoki
- The Feinstein Institutes for Medical Research at Northwell, Manhasset, NY, United States
| | - Yu Okuma
- The Feinstein Institutes for Medical Research at Northwell, Manhasset, NY, United States.,Department of Neurological Surgery at Fukuyama City Hospital, Fukuyama, Japan
| | - Lance B Becker
- The Feinstein Institutes for Medical Research at Northwell, Manhasset, NY, United States.,Department of Emergency Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Kei Hayashida
- The Feinstein Institutes for Medical Research at Northwell, Manhasset, NY, United States
| | - Koichiro Shinozaki
- The Feinstein Institutes for Medical Research at Northwell, Manhasset, NY, United States.,Department of Emergency Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
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13
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Long N, Min JE, Anh NH, Kim SJ, Park S, Kim HM, Yoon SJ, Lim J, Lee SJ, Kwon SW. Isolation and Metabolic Assessment of Cancer Cell Mitochondria. ACS OMEGA 2020; 5:27304-27313. [PMID: 33134693 PMCID: PMC7594158 DOI: 10.1021/acsomega.0c03612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Mitochondrial metabolism plays an essential role in various biological processes of cancer cells. Herein, we established an experimental procedure for the metabolic assessment of mitochondria in cancer cells. We examined procedures for mitochondrial isolation coupled with various mitochondrial extraction buffers in three major cancer cell lines (PANC1, A549, and MDA-MB-231) and identified a potentially optimal and generalized approach. The purity of the mitochondrial fraction isolated by the selected protocol was verified using specific protein markers of cellular components, and the ultrastructure of the isolated mitochondria was also analyzed by transmission electron microscopy. The isolation procedure, involving a bead beater for cell lysis, a modified sucrose buffer, and differential centrifugation, appeared to be a suitable method for the extraction of mitochondria from cancer cells. Electron micrographs indicated an intact two-layer membrane and inner structures of mitochondria isolated by this procedure. Metabolomic and lipidomic analyses were conducted to examine the metabolic phenotypes of the mitochondria-enriched fractions and associated bulk cancer cells. A total of 44 metabolites, including malate and succinate, occurred at significantly higher levels in the mitochondrial fractions, whereas 51 metabolites, including citrate, oxaloacetate, and fumarate of the Krebs cycle and the oncometabolites glutamine and glutamate, were reduced in mitochondria compared to that in the corresponding bulk cells of PANC1. Similar patterns were observed in mitochondria and bulk cells of MDA-MB-231 and A549 cell lines. A clear difference between the lipid profiles of bulk PANC1, MDA-MB-231, and A549 and corresponding mitochondrial fractions of these cell lines was detected by principal component analysis. In conclusion, we developed an experimental procedure for a large-scale metabolic assessment for suborganelle metabolic profiling and multiple omics data integration in cancer cells with broad applications.
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Affiliation(s)
- Nguyen
Phuoc Long
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung Eun Min
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Nguyen Hoang Anh
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun Jo Kim
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongoh Park
- Department
of Statistics, Sungshin Women’s University, Seoul 02844, Republic of Korea
| | - Hyung Min Kim
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Jun Yoon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Johan Lim
- Department
of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Seul Ji Lee
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Won Kwon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Plant
Genomics and Breeding Institute, Seoul National
University, Seoul 08826, Republic of Korea
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14
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Novel approach to quantify mitochondrial content and intrinsic bioenergetic efficiency across organs. Sci Rep 2020; 10:17599. [PMID: 33077793 PMCID: PMC7572412 DOI: 10.1038/s41598-020-74718-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/05/2020] [Indexed: 01/09/2023] Open
Abstract
Human disease pathophysiology commonly involves metabolic disruption at both the cellular and subcellular levels. Isolated mitochondria are a powerful model for separating global cellular changes from intrinsic mitochondrial alterations. However, common laboratory practices for isolating mitochondria (e.g., differential centrifugation) routinely results in organelle preparations with variable mitochondrial purity. To overcome this issue, we developed a mass spectrometry-based method that quantitatively evaluates sample-specific percent mitochondrial enrichment. Sample-specific mitochondrial enrichment was then used to correct various biochemical readouts of mitochondrial function to a ‘fixed’ amount of mitochondrial protein, thus allowing for intrinsic mitochondrial bioenergetics, relative to the underlying proteome, to be assessed across multiple mouse tissues (e.g., heart, brown adipose, kidney, liver). Our results support the use of mitochondrial-targeted nLC-MS/MS as a method to quantitate mitochondrial enrichment on a per-sample basis, allowing for unbiased comparison of functional parameters between populations of mitochondria isolated from metabolically distinct tissues. This method can easily be applied across multiple experimental settings in which intrinsic shifts in the mitochondrial network are suspected of driving a given physiological or pathophysiological outcome.
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15
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Borah K, Rickman OJ, Voutsina N, Ampong I, Gao D, Baple EL, Dias IH, Crosby AH, Griffiths HR. A quantitative LC-MS/MS method for analysis of mitochondrial -specific oxysterol metabolism. Redox Biol 2020; 36:101595. [PMID: 32574926 PMCID: PMC7317222 DOI: 10.1016/j.redox.2020.101595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Oxysterols are critical regulators of inflammation and cholesterol metabolism in cells. They are oxidation products of cholesterol and may be differentially metabolised in subcellular compartments and in biological fluids. New analytical methods are needed to improve our understanding of oxysterol trafficking and the molecular interplay between the cellular compartments required to maintain cholesterol/oxysterol homeostasis. Here we describe a method for isolation of oxysterols using solid phase extraction and quantification by liquid chromatography-mass spectrometry, applied to tissue, cells and mitochondria. We analysed five monohydroxysterols; 24(S)-hydroxycholesterol, 25-hydroxycholesterol, 27-hydroxycholesterol, 7α-hydroxycholesterol, 7 ketocholesterol and three dihydroxysterols 7α-24(S)dihydroxycholesterol, 7α-25dihydroxycholesterol, 7α-27dihydroxycholesterol by LC-MS/MS following reverse phase chromatography. Our new method, using Triton and DMSO extraction, shows improved extraction efficiency and recovery of oxysterols from cellular matrix. We validated our method by reproducibly measuring oxysterols in mouse brain tissue and showed that mice fed a high fat diet had significantly lower levels of 24S/25diOHC, 27diOHC and 7ketoOHC. We measured oxysterols in mitochondria from peripheral blood mononuclear cells and highlight the importance of rapid cell isolation to minimise effects of handling and storage conditions on oxysterol composition in clinical samples. In addition, in vitro cell culture systems, of THP-1 monocytes and neuronal-like SH-SH5Y cells, showed mitochondrial-specific oxysterol metabolism and profiles were lineage specific. In summary, we describe a robust and reproducible method validated for improved recovery, quantitative linearity and detection, reproducibility and selectivity for cellular oxysterol analysis. This method enables subcellular oxysterol metabolism to be monitored and is versatile in its application to various biological and clinical samples.
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Affiliation(s)
- Khushboo Borah
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Olivia J Rickman
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Nikol Voutsina
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Isaac Ampong
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Dan Gao
- Department of Human Anatomy,Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Emma L Baple
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | | | - Andrew H Crosby
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Helen R Griffiths
- Department of Nutrition, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK.
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16
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van der Walt G, Louw R. Novel mitochondrial and cytosolic purification pipeline for compartment-specific metabolomics in mammalian disease model tissues. Metabolomics 2020; 16:78. [PMID: 32577914 DOI: 10.1007/s11306-020-01697-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/13/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mitochondria represent an important milieu for studying the pathogenesis of several major diseases. The need for organelle-level metabolic resolution exists, as mitochondrial/cytosolic metabolites are often diluted beyond detection limits in complex samples. Compartment-specific studies are still hindered by the lack of efficient, cost-effective fractioning methods-applicable to laboratories of all financial/analytical standing. OBJECTIVES We established a novel mitochondrial/cytosolic purification pipeline for complimentary GC-TOF-MS and 1H-NMR metabolomics using robust, commercially available fractionation strategies. METHODS Magnetic based mitochondria isolation kits (MACS) were adapted for this purpose, accompanied by cytosolic filtering. Yield was assessed through the percentage recovery of citrate synthase (CS; a mitochondrial marker), purity by immunoblotting against compartment-specific proteins and integrity interrogated through the respiratory coupling ratio (RCR). The effects of the kit-based buffers on MS/NMR analyses of pure metabolite standards were evaluated. Finally, biological applicability to mammalian disease models was shown using Ndufs4 mouse brain tissue. RESULTS With minor modifications, MACS produced around 60% more mitochondria compared to a differential centrifugation method. Less than 15% of lysosomal LAMP-2 protein was found in the MACS isolates, confirming relative purity-while RCR's above 6 indicate sufficient mitochondrial integrity. The filtering approach effectively depleted mitochondria from the cytosolic fraction, as indicated by negligible Hsp60 and CS levels. Our GC-MS pilot yielded 60-70 features per fraction, while NMR analyses could quantify 6-10 of the most abundant compounds in each fraction. CONCLUSION This study provides a simple and flexible solution for mitochondrial and cytosolic metabolomics in animal model tissues, towards large-scale application of such methodologies in disease research.
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Affiliation(s)
- Gunter van der Walt
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa
| | - Roan Louw
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), Private Bag X6001, Potchefstroom, South Africa.
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17
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Levitsky Y, Hammer SS, Fisher KP, Huang C, Gentles TL, Pegouske DJ, Xi C, Lydic TA, Busik JV, Proshlyakov DA. Mitochondrial Ceramide Effects on the Retinal Pigment Epithelium in Diabetes. Int J Mol Sci 2020; 21:ijms21113830. [PMID: 32481596 PMCID: PMC7312467 DOI: 10.3390/ijms21113830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial damage in the cells comprising inner (retinal endothelial cells) and outer (retinal pigment epithelium (RPE)) blood–retinal barriers (BRB) is known to precede the initial BRB breakdown and further histopathological abnormalities in diabetic retinopathy (DR). We previously demonstrated that activation of acid sphingomyelinase (ASM) is an important early event in the pathogenesis of DR, and recent studies have demonstrated that there is an intricate connection between ceramide and mitochondrial function. This study aimed to determine the role of ASM-dependent mitochondrial ceramide accumulation in diabetes-induced RPE cell damage. Mitochondria isolated from streptozotocin (STZ)-induced diabetic rat retinas (7 weeks duration) showed a 1.64 ± 0.29-fold increase in the ceramide-to-sphingomyelin ratio compared to controls. Conversely, the ceramide-to-sphingomyelin ratio was decreased in the mitochondria isolated from ASM-knockout mouse retinas compared to wild-type littermates, confirming the role of ASM in mitochondrial ceramide production. Cellular ceramide was elevated 2.67 ± 1.07-fold in RPE cells derived from diabetic donors compared to control donors, and these changes correlated with increased gene expression of IL-1β, IL-6, and ASM. Treatment of RPE cells derived from control donors with high glucose resulted in elevated ASM, vascular endothelial growth factor (VEGF), and intercellular adhesion molecule 1 (ICAM-1) mRNA. RPE from diabetic donors showed fragmented mitochondria and a 2.68 ± 0.66-fold decreased respiratory control ratio (RCR). Treatment of immortalized cell in vision research (ARPE-19) cells with high glucose resulted in a 25% ± 1.6% decrease in citrate synthase activity at 72 h. Inhibition of ASM with desipramine (15 μM, 1 h daily) abolished the decreases in metabolic functional parameters. Our results are consistent with diabetes-induced increase in mitochondrial ceramide through an ASM-dependent pathway leading to impaired mitochondrial function in the RPE cells of the retina.
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Affiliation(s)
- Yan Levitsky
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; (D.J.P.); (C.X.)
| | - Sandra S. Hammer
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
| | - Kiera P. Fisher
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
| | - Chao Huang
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
| | - Travan L. Gentles
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
| | - David J. Pegouske
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; (D.J.P.); (C.X.)
| | - Caimin Xi
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; (D.J.P.); (C.X.)
| | - Todd A. Lydic
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
| | - Julia V. Busik
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (Y.L.); (S.S.H.); (K.P.F.); (C.H.); (T.L.G.); (T.A.L.)
- Correspondence: (J.V.B.); (D.A.P.); Tel.: +1-517-884-5118 (J.V.B.); +1-517-353-1117 (D.A.P.)
| | - Denis A. Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; (D.J.P.); (C.X.)
- Correspondence: (J.V.B.); (D.A.P.); Tel.: +1-517-884-5118 (J.V.B.); +1-517-353-1117 (D.A.P.)
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18
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The uricosuric benzbromarone disturbs the mitochondrial redox homeostasis and activates the NRF2 signaling pathway in HepG2 cells. Free Radic Biol Med 2020; 152:216-226. [PMID: 32198009 DOI: 10.1016/j.freeradbiomed.2020.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/08/2020] [Accepted: 03/12/2020] [Indexed: 11/25/2022]
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19
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Wheeler S, Sillence DJ. Niemann-Pick type C disease: cellular pathology and pharmacotherapy. J Neurochem 2019; 153:674-692. [PMID: 31608980 DOI: 10.1111/jnc.14895] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/10/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022]
Abstract
Niemann-Pick type C disease (NPCD) was first described in 1914 and affects approximately 1 in 150 000 live births. It is characterized clinically by diverse symptoms affecting liver, spleen, motor control, and brain; premature death invariably results. Its molecular origins were traced, as late as 1997, to a protein of late endosomes and lysosomes which was named NPC1. Mutation or absence of this protein leads to accumulation of cholesterol in these organelles. In this review, we focus on the intracellular events that drive the pathology of this disease. We first introduce endocytosis, a much-studied area of dysfunction in NPCD cells, and survey the various ways in which this process malfunctions. We briefly consider autophagy before attempting to map the more complex pathways by which lysosomal cholesterol storage leads to protein misregulation, mitochondrial dysfunction, and cell death. We then briefly introduce the metabolic pathways of sphingolipids (as these emerge as key species for treatment) and critically examine the various treatment approaches that have been attempted to date.
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Affiliation(s)
- Simon Wheeler
- School of Pharmacy, De Montfort University, The Gateway, Leicester, UK
| | - Dan J Sillence
- School of Pharmacy, De Montfort University, The Gateway, Leicester, UK
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20
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Kappler L, Lehmann R. Mass-spectrometric multi-omics linked to function – State-of-the-art investigations of mitochondria in systems medicine. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Kappler L, Hoene M, Hu C, von Toerne C, Li J, Bleher D, Hoffmann C, Böhm A, Kollipara L, Zischka H, Königsrainer A, Häring HU, Peter A, Xu G, Sickmann A, Hauck SM, Weigert C, Lehmann R. Linking bioenergetic function of mitochondria to tissue-specific molecular fingerprints. Am J Physiol Endocrinol Metab 2019; 317:E374-E387. [PMID: 31211616 DOI: 10.1152/ajpendo.00088.2019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondria are dynamic organelles with diverse functions in tissues such as liver and skeletal muscle. To unravel the mitochondrial contribution to tissue-specific physiology, we performed a systematic comparison of the mitochondrial proteome and lipidome of mice and assessed the consequences hereof for respiration. Liver and skeletal muscle mitochondrial protein composition was studied by data-independent ultra-high-performance (UHP)LC-MS/MS-proteomics, and lipid profiles were compared by UHPLC-MS/MS lipidomics. Mitochondrial function was investigated by high-resolution respirometry in samples from mice and humans. Enzymes of pyruvate oxidation as well as several subunits of complex I, III, and ATP synthase were more abundant in muscle mitochondria. Muscle mitochondria were enriched in cardiolipins associated with higher oxidative phosphorylation capacity and flexibility, in particular CL(18:2)4 and 22:6-containing cardiolipins. In contrast, protein equipment of liver mitochondria indicated a shuttling of complex I substrates toward gluconeogenesis and ketogenesis and a higher preference for electron transfer via the flavoprotein quinone oxidoreductase pathway. Concordantly, muscle and liver mitochondria showed distinct respiratory substrate preferences. Muscle respired significantly more on the complex I substrates pyruvate and glutamate, whereas in liver maximal respiration was supported by complex II substrate succinate. This was a consistent finding in mouse liver and skeletal muscle mitochondria and human samples. Muscle mitochondria are tailored to produce ATP with a high capacity for complex I-linked substrates. Liver mitochondria are more connected to biosynthetic pathways, preferring fatty acids and succinate for oxidation. The physiologic diversity of mitochondria may help to understand tissue-specific disease pathologies and to develop therapies targeting mitochondrial function.
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Affiliation(s)
- Lisa Kappler
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Miriam Hoene
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Chunxiu Hu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | | | - Jia Li
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Daniel Bleher
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Christoph Hoffmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Anja Böhm
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
- German Center for Diabetes Research, Tuebingen, Germany
| | | | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Institute of Toxicology and Environmental Hygiene, Technical University Munich, Munich, Germany
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site, Tuebingen, Germany
| | - Hans-Ulrich Häring
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
- German Center for Diabetes Research, Tuebingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
- German Center for Diabetes Research, Tuebingen, Germany
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS, Dortmund, Germany
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Munich, Germany
- German Center for Diabetes Research, Tuebingen, Germany
| | - Cora Weigert
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
- German Center for Diabetes Research, Tuebingen, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tuebingen, Tuebingen, Germany
- German Center for Diabetes Research, Tuebingen, Germany
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22
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Fractionated mitochondrial magnetic separation for isolation of synaptic mitochondria from brain tissue. Sci Rep 2019; 9:9656. [PMID: 31273236 PMCID: PMC6609636 DOI: 10.1038/s41598-019-45568-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
While mitochondria maintain essential cellular functions, such as energy production, calcium homeostasis, and regulating programmed cellular death, they also play a major role in pathophysiology of many neurological disorders. Furthermore, several neurodegenerative diseases are closely linked with synaptic damage and synaptic mitochondrial dysfunction. Unfortunately, the ability to assess mitochondrial dysfunction and the efficacy of mitochondrial-targeted therapies in experimental models of neurodegenerative disease and CNS injury is limited by current mitochondrial isolation techniques. Density gradient ultracentrifugation (UC) is currently the only technique that can separate synaptic and non-synaptic mitochondrial sub-populations, though small brain regions cannot be assayed due to low mitochondrial yield. To address this limitation, we used fractionated mitochondrial magnetic separation (FMMS), employing magnetic anti-Tom22 antibodies, to develop a novel strategy for isolation of functional synaptic and non-synaptic mitochondria from mouse cortex and hippocampus without the usage of UC. We compared the yield and functionality of mitochondria derived using FMMS to those derived by UC. FMMS produced 3x more synaptic mitochondrial protein yield compared to UC from the same amount of tissue, a mouse hippocampus. FMMS also has increased sensitivity, compared to UC separation, to measure decreased mitochondrial respiration, demonstrated in a paradigm of mild closed head injury. Taken together, FMMS enables improved brain-derived mitochondrial yield for mitochondrial assessments and better detection of mitochondrial impairment in CNS injury and neurodegenerative disease.
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23
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Veyrat-Durebex C, Bris C, Codron P, Bocca C, Chupin S, Corcia P, Vourc'h P, Hergesheimer R, Cassereau J, Funalot B, Andres CR, Lenaers G, Couratier P, Reynier P, Blasco H. Metabo-lipidomics of Fibroblasts and Mitochondrial-Endoplasmic Reticulum Extracts from ALS Patients Shows Alterations in Purine, Pyrimidine, Energetic, and Phospholipid Metabolisms. Mol Neurobiol 2019; 56:5780-5791. [PMID: 30680691 DOI: 10.1007/s12035-019-1484-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/10/2019] [Indexed: 12/16/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by a wide metabolic remodeling, as shown by recent metabolomics and lipidomics studies performed in samples from patient cohorts and experimental animal models. Here, we explored the metabolome and lipidome of fibroblasts from sporadic ALS patients (n = 13) comparatively to age- and sex-matched controls (n = 11), and the subcellular fraction containing the mitochondria and endoplasmic reticulum (mito-ER), given that mitochondrial dysfunctions and ER stress are important features of ALS patho-mechanisms. We also assessed the mitochondrial oxidative respiration and the mitochondrial genomic (mtDNA) sequence, although without yielding significant differences. Compared to controls, ALS fibroblasts did not exhibit a mitochondrial respiration defect nor an increased proportion of mitochondrial DNA mutations. In addition, non-targeted metabolomics and lipidomics analyses identified 124 and 127 metabolites, and 328 and 220 lipids in whole cells and the mito-ER fractions, respectively, along with partial least-squares-discriminant analysis (PLS-DA) models being systematically highly predictive of the disease. The most discriminant metabolomic features were the alteration of purine, pyrimidine, and energetic metabolisms, suggestive of oxidative stress and of pro-inflammatory status. The most important lipidomic feature in the mito-ER fraction was the disturbance of phosphatidylcholine PC (36:4p) levels, which we had previously reported in the cerebrospinal fluid of ALS patients and in the brain from an ALS mouse model. Thus, our results reveal that fibroblasts from sporadic ALS patients share common metabolic remodeling, consistent with other metabolic studies performed in ALS, opening perspectives for further exploration in this cellular model in ALS.
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Affiliation(s)
- Charlotte Veyrat-Durebex
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France. .,Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France. .,Laboratoire de Biochimie et Biologie Moléculaire, CHRU Hôpital Bretonneau, 2, Bd Tonnellé, 37044, Tours, France.
| | - Céline Bris
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France.,Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France
| | - Philippe Codron
- Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France.,Centre de Ressources et de Compétences SLA, Service de Neurologie, CHU Angers, Angers, France
| | - Cinzia Bocca
- Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France
| | - Stéphanie Chupin
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Philippe Corcia
- Université de Tours, Inserm U1253, Tours, France.,Centre de Référence SLA, Service de Neurologie, CHRU Bretonneau, Tours, France.,Fédération des CRCSLA Tours et Limoges, LITORALS, Tours, France
| | - Patrick Vourc'h
- Laboratoire de Biochimie et Biologie Moléculaire, CHRU Hôpital Bretonneau, 2, Bd Tonnellé, 37044, Tours, France.,Université de Tours, Inserm U1253, Tours, France
| | | | - Julien Cassereau
- Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France.,Centre de Ressources et de Compétences SLA, Service de Neurologie, CHU Angers, Angers, France
| | - Benoit Funalot
- Fédération des CRCSLA Tours et Limoges, LITORALS, Tours, France
| | - Christian R Andres
- Laboratoire de Biochimie et Biologie Moléculaire, CHRU Hôpital Bretonneau, 2, Bd Tonnellé, 37044, Tours, France.,Université de Tours, Inserm U1253, Tours, France
| | - Guy Lenaers
- Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France
| | | | - Pascal Reynier
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France.,Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France
| | - Hélène Blasco
- Unité Mixte de Recherche MITOVASC, CNRS 6015-INSERM 1083, Université d'Angers, Angers, France. .,Laboratoire de Biochimie et Biologie Moléculaire, CHRU Hôpital Bretonneau, 2, Bd Tonnellé, 37044, Tours, France. .,Université de Tours, Inserm U1253, Tours, France.
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24
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Kappler L, Kollipara L, Lehmann R, Sickmann A. Investigating the Role of Mitochondria in Type 2 Diabetes - Lessons from Lipidomics and Proteomics Studies of Skeletal Muscle and Liver. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:143-182. [PMID: 31452140 DOI: 10.1007/978-981-13-8367-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is discussed as a key player in the pathogenesis of type 2 diabetes mellitus (T2Dm), a highly prevalent disease rapidly developing as one of the greatest global health challenges of this century. Data however about the involvement of mitochondria, central hubs in bioenergetic processes, in the disease development are still controversial. Lipid and protein homeostasis are under intense discussion to be crucial for proper mitochondrial function. Consequently proteomics and lipidomics analyses might help to understand how molecular changes in mitochondria translate to alterations in energy transduction as observed in the healthy and metabolic diseases such as T2Dm and other related disorders. Mitochondrial lipids integrated in a tool covering proteomic and functional analyses were up to now rarely investigated, although mitochondrial lipids might provide a possible lynchpin in the understanding of type 2 diabetes development and thereby prevention. In this chapter state-of-the-art analytical strategies, pre-analytical aspects, potential pitfalls as well as current proteomics and lipidomics-based knowledge about the pathophysiological role of mitochondria in the pathogenesis of type 2 diabetes will be discussed.
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Affiliation(s)
- Lisa Kappler
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tuebingen, Tuebingen, Germany.,German Center for Diabetes Research (DZD e.V.), Tuebingen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany. .,Medical Proteome Centre, Ruhr Universität Bochum, Bochum, Germany. .,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK.
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25
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Yamamoto T, Tsunoda M, Ozono M, Watanabe A, Kotake K, Hiroshima Y, Yamada A, Terada H, Shinohara Y. Polyethyleneimine renders mitochondrial membranes permeable by interacting with negatively charged phospholipids in them. Arch Biochem Biophys 2018; 652:9-17. [PMID: 29886045 DOI: 10.1016/j.abb.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 01/21/2023]
Abstract
Polyethyleneimines (PEIs) are used for transfection of cells with nucleic acids. Meanwhile, the interaction of PEI with mitochondria causes cytochrome c release prior to apoptosis; the mechanisms how PEI causes this permeabilization of mitochondrial membranes and the release of cytochrome c remain unclear. To clarify these mechanisms, we examined the effects of branched-type PEI and linear-type PEI, each of which was 25 kDa in size, on mitochondria. The permeabilization potency of mitochondrial membranes by branched PEI was stronger than that by linear PEI. The permeabilization by PEIs were insensitive to permeability-transition inhibitors, indicating that PEI-induced permeabilization was not attributed to permeability transition. Meanwhile, PEIs caused permeabilization of artificial lipid vesicles; again, the permeabilization potency of branched PEI was stronger than that of linear PEI. Such a difference in this potency was close to that in the case of isolated mitochondria, signifying that the PEI-induced permeabilization of mitochondrial membranes could be attributed to PEI's interaction with the phospholipid phase. Furthermore, this PEI-induced permeabilization of the lipid vesicles was observed only in the case of lipid vesicles including negatively charged phospholipids. These results indicate that PEIs interacted with negatively charged phospholipids in the mitochondrial membranes to directly lead to their permeabilization.
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Affiliation(s)
- Takenori Yamamoto
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan.
| | - Moe Tsunoda
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan
| | - Mizune Ozono
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan
| | - Akira Watanabe
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan
| | - Kazumasa Kotake
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan
| | - Yuka Hiroshima
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan
| | - Akiko Yamada
- School of Dentistry, Tokushima University, Kuramotocho-3, Tokushima 770-8504, Japan
| | - Hiroshi Terada
- Niigata University of Pharmacy and Applied Life Sciences, Niigata City 956-8603, Japan
| | - Yasuo Shinohara
- Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, Tokushima University, Shomachi-1, Tokushima 770-8505, Japan
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26
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Afanasyeva MA, Ustiugova AS, Golyshev SA, Kopylov AT, Bogolyubova AV, Demin DE, Belousov PV, Schwartz AM. Isolation of Large Amounts of Highly Pure Mitochondria for "Omics" Studies. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29534672 DOI: 10.1134/s0006297918010108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Ultracentrifugation on a density gradient remains the only reliable way to obtain highly pure mitochondria preparations. However, it is not readily available for any laboratory and has a serious disadvantage of providing low mitochondria yield, which can be critical when working with limited starting material. Here we describe a combined method for isolation of mitochondria for proteomic studies that includes cell disruption by sonication, differential centrifugation, and magnetic separation. Our method provides remarkable enrichment of mitochondrial proteins as compared to differential centrifugation, magnetic separation, or their combination, and it enables the strongest depletion of cytoplasmic components, as assessed by two-dimensional electrophoresis, mass spectrometry, and Western blot. It also doubles the yield of mitochondria. However, our method should not be used for functional studies as most of the isolated organelles demonstrate disturbed structure in electron microphotographs.
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Affiliation(s)
- M A Afanasyeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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27
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Geiger J, Dalgaard LT. Isolation and Analysis of Mitochondrial Small RNAs from Rat Liver Tissue and HepG2 Cells. Methods Mol Biol 2018; 1782:337-350. [PMID: 29851010 DOI: 10.1007/978-1-4939-7831-1_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The presence of noncoding RNAs, such as microRNAs (miRNAs), in mitochondria has been reported by several studies. The biological roles and functions of these mitochondrial miRNAs ("mitomiRs") have not been sufficiently characterized, but the mitochondrial localization of miRNAs has recently gained significance due to modified mitomiR-populations in certain states of diseases. Here, we describe the isolation and analysis of mitochondrial RNAs from rat liver tissue and HepG2 cells. The principle of the analysis is to prepare mitochondria by differential centrifugation. Cytosolic RNA contamination is eliminated by RNase A treatment followed by Percoll gradient purification and RNA extraction. Small RNA content is verified by capillary electrophoresis. Mitochondrial miRNAs are detected by qPCR following synthesis of cDNA. After qPCR-based mitomiR-profiling, the Normfinder algorithm is applied to identify the suitable reference miRNAs to use as normalizers for mitochondrial input and data analysis. The described procedure depicts a simple way of isolating and quantifying mitomiRs in tissue and cell culture samples.
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Affiliation(s)
- Julian Geiger
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
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28
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Liu X, Xu G. Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review. Anal Chim Acta 2017; 1037:3-12. [PMID: 30292306 DOI: 10.1016/j.aca.2017.11.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023]
Abstract
Metabolomics and lipidomics generally targets a huge number of intermediate and end products of cellular metabolism in body fluids, tissues, and cells etc. At present, mass spectrometry (MS) based metabolic or lipid profiling of routine biological specimens including the whole cells, tissues, plasma, serum and urine etc., can cover hundreds of metabolites or lipid species in one analysis, which has qualified deep elucidation of global metabolic and lipid networks. Mitochondria are important intracellular organelles and many critical biochemical reactions occur here, they provide building block for new cells, control redox balance, participate in apoptosis and behave as a signalling platform. Evidence suggests high prevalence of mitochondrial dysfunction occurs in a variety of cancers and other diseases, thus there is an urgent demand for investigating and clarifying mitochondrial metabolic and lipid alterations induced by diseases. Nevertheless, mitochondria contribute a small fraction to cellular contents, profiling of whole cell is probably unsuitable for monitoring alterations in mitochondria. Therefore, metabolomics and lipidomics analyses specially for mitochondria are necessary to understand disturbed metabolic and lipid pathways induced by environment and diseases. However, methods for comprehensively profiling metabolites and lipids in mitochondria have been limited at present. This review summarizes the current states and progress of MS-based mitochondrial metabolomics and lipidomics study. Details of mitochondrial isolation procedure, analytical methods and their applications are described. The challenges and opportunities are also given.
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Affiliation(s)
- Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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29
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Veyrat-Durebex C, Bocca C, Chupin S, Kouassi Nzoughet J, Simard G, Lenaers G, Reynier P, Blasco H. Metabolomics and Lipidomics Profiling of a Combined Mitochondrial Plus Endoplasmic Reticulum Fraction of Human Fibroblasts: A Robust Tool for Clinical Studies. J Proteome Res 2017; 17:745-750. [PMID: 29111762 DOI: 10.1021/acs.jproteome.7b00637] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts. We applied combined metabolomics and lipidomics analyses by mass spectrometry with excellent reproducibility. Seventy-two metabolites and 418 complex lipids were detected with a mean coefficient of variation around 12%, among which many were specific to the mitochondrial metabolism. Thus this strategy based on robust mitochondria-ER extraction and "omics" combination will be useful for investigating the pathophysiology of complex diseases.
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Affiliation(s)
- Charlotte Veyrat-Durebex
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France.,Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Cinzia Bocca
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Stéphanie Chupin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France
| | - Judith Kouassi Nzoughet
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Gilles Simard
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France
| | - Guy Lenaers
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France.,Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Hélène Blasco
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France.,Université François-Rabelais , INSERM U930, 37000 Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , 37044 Tours, France
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30
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Rostovtseva TK, Hoogerheide DP, Rovini A, Bezrukov SM. Lipids in Regulation of the Mitochondrial Outer Membrane Permeability, Bioenergetics, and Metabolism. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-55539-3_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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