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Heineman BD, Liu X, Wu GY. Targeted Mitochondrial Delivery to Hepatocytes: A Review. J Clin Transl Hepatol 2022; 10:321-328. [PMID: 35528979 PMCID: PMC9039707 DOI: 10.14218/jcth.2021.00093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/22/2021] [Accepted: 09/15/2021] [Indexed: 12/04/2022] Open
Abstract
Defects in mitochondria are responsible for various genetic and acquired diseases. Mitochondrial transplantation, a method that involves introduction of healthy donor mitochondria into cells with dysfunctional mitochondria, could offer a novel approach to treat such diseases. Some studies have demonstrated the therapeutic benefit of mitochondrial transplantation and targeted delivery in vivo and in vitro within hepatocytes and the liver. This review discusses the issues regarding isolation and delivery of mitochondria to hepatocytes and the liver, and examines the existing literature in order to elucidate the utility and practicality of mitochondrial transplantation in the treatment of liver disease. Studies reviewed demonstrate that mitochondrial uptake could specifically target hepatocytes, address the challenge of non-specific localization of donor mitochondria, and provide evidence of changes in liver function following injection of mitochondria into mouse and rat disease models. While potential benefits and advantages of mitochondrial transplantation are evident, more research is needed to determine the practicality of mitochondrial transplantation for the treatment of genetic and acquired liver diseases.
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Affiliation(s)
- Brent D. Heineman
- Correspondence to: Brent D. Heineman, 8 Talcott Forest Rd, Farmington Apt. M, Farmington, CT 06032, USA. ORCID: https://orcid.org/0000-0003-3867-1216. Tel: +1-860-986-2943, Fax: +1-860-679-6582, E-mail:
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2
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Jiang X, Liu S, Zhang Y, Ji Y, Sohail A, Cao C, Wang P, Xiao H. Free-Flow Isoelectric Focusing for Comprehensive Separation and Analysis of Human Salivary Microbiome for Lung Cancer. Anal Chem 2020; 92:12017-12025. [DOI: 10.1021/acs.analchem.0c02627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Pharmaceutical Co., Ltd., Nanjing 210042, Jiangsu, China
| | - Amir Sohail
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Pharmaceutical Co., Ltd., Nanjing 210042, Jiangsu, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Farah NK, Liu X, Wu CH, Wu GY. An Improved Method for Preparation of Uniform and Functional Mitochondria from Fresh Liver. J Clin Transl Hepatol 2019; 7:46-50. [PMID: 30944819 PMCID: PMC6441644 DOI: 10.14218/jcth.2018.00064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/28/2019] [Indexed: 12/12/2022] Open
Abstract
Background and Aims: As the major energy source for mammalian cells, mitochondria have been the subject of numerous studies. However, the isolation and purification of healthy mitochondria, especially from fresh tissue, remains challenging. The most popular methods and kits involve various centrifugation steps which require substantial time and equipment but do not consistently provide pure preparations of functional mitochondria. The aim of this study was to determine whether methods could be devised to improve the purity and yield of functional mitochondria from fresh tissue. Methods: Fresh mouse liver was homogenized, and cells lysed. Particle size analysis, quantitation of mitochondrial DNA, mitochondrial oxygen consumption, and purity of mitochondria (by electron microscopy) were measured in samples after various purification steps and significant differences determined. Results: A two-step procedure consisting of centrifugation followed by filtration through 1.2μ and 0.8μ filters resulted in uniform mitochondrial preparations with diameters between 520-540 nm, and approximately 5-times more pure samples. The mitochondria thus obtained had oxygen consumption and sensitivities to mitochondrial inhibitors that were indistinguishable from those purified by centrifugation alone. Electron microscopy confirmed the presence of more uniform and 4-5 times greater concentrations of mitochondria compared to centrifugation alone. Conclusions: A two-step procedure consisting of sequential centrifugation followed by filtration is a rapid method for the production of highly purified, uniform and functional mitochondria.
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Affiliation(s)
- Nagham Khouri Farah
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
| | - Xiaocong Liu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
- *Correspondence to: Xiaocong Liu, Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT 06030, USA. Tel: +1-860-679-2509, Fax: +860-679-6582, E-mail:
| | - Catherine H. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
| | - George Y. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
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Polishchuk EV, Merolla A, Lichtmannegger J, Romano A, Indrieri A, Ilyechova EY, Concilli M, De Cegli R, Crispino R, Mariniello M, Petruzzelli R, Ranucci G, Iorio R, Pietrocola F, Einer C, Borchard S, Zibert A, Schmidt HH, Di Schiavi E, Puchkova LV, Franco B, Kroemer G, Zischka H, Polishchuk RS. Activation of Autophagy, Observed in Liver Tissues From Patients With Wilson Disease and From ATP7B-Deficient Animals, Protects Hepatocytes From Copper-Induced Apoptosis. Gastroenterology 2019; 156:1173-1189.e5. [PMID: 30452922 DOI: 10.1053/j.gastro.2018.11.032] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 10/23/2018] [Accepted: 11/10/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Wilson disease (WD) is an inherited disorder of copper metabolism that leads to copper accumulation and toxicity in the liver and brain. It is caused by mutations in the adenosine triphosphatase copper transporting β gene (ATP7B), which encodes a protein that transports copper from hepatocytes into the bile. We studied ATP7B-deficient cells and animals to identify strategies to decrease copper toxicity in patients with WD. METHODS We used RNA-seq to compare gene expression patterns between wild-type and ATP7B-knockout HepG2 cells exposed to copper. We collected blood and liver tissues from Atp7b-/- and Atp7b+/- (control) rats (LPP) and mice; some mice were given 5 daily injections of an autophagy inhibitor (spautin-1) or vehicle. We obtained liver biopsies from 2 patients with WD in Italy and liver tissues from patients without WD (control). Liver tissues were analyzed by immunohistochemistry, immunofluorescence, cell viability, apoptosis assays, and electron and confocal microscopy. Proteins were knocked down in cell lines using small interfering RNAs. Levels of copper were measured in cell lysates, blood samples, liver homogenates, and subcellular fractions by spectroscopy. RESULTS After exposure to copper, ATP7B-knockout cells had significant increases in the expression of 103 genes that regulate autophagy (including MAP1LC3A, known as LC3) compared with wild-type cells. Electron and confocal microscopy visualized more autophagic structures in the cytoplasm of ATP7B-knockout cells than wild-type cells after copper exposure. Hepatocytes in liver tissues from patients with WD and from Atp7b-/- mice and rats (but not controls) had multiple autophagosomes. In ATP7B-knockout cells, mammalian target of rapamycin (mTOR) had decreased activity and was dissociated from lysosomes; this resulted in translocation of the mTOR substrate transcription factor EB to the nucleus and activation of autophagy-related genes. In wild-type HepG2 cells (but not ATP7B-knockout cells), exposure to copper and amino acids induced recruitment of mTOR to lysosomes. Pharmacologic inhibitors of autophagy or knockdown of autophagy proteins ATG7 and ATG13 induced and accelerated the death of ATP7B-knockout HepG2 cells compared with wild-type cells. Autophagy protected ATP7B-knockout cells from copper-induced death. CONCLUSION ATP7B-deficient hepatocytes, such as in those in patients with WD, activate autophagy in response to copper overload to prevent copper-induced apoptosis. Agents designed to activate this autophagic pathway might decrease copper toxicity in patients with WD.
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Affiliation(s)
- Elena V Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; ITMO University, St. Petersburg, Russia; Institute of Biosciences and Bioresources CNR, Italy
| | - Assunta Merolla
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Josef Lichtmannegger
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Alessia Romano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Alessia Indrieri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Translational Medical Science, "Federico II" University of Naples, Naples, Italy
| | - Ekaterina Y Ilyechova
- ITMO University, St. Petersburg, Russia; Department of Molecular Genetics, Institute of Experimental Medicine, St. Petersburg, Russia
| | - Mafalda Concilli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Roberta Crispino
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Marta Mariniello
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | | | - Giusy Ranucci
- Division of Metabolism, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Raffaele Iorio
- Department of Translational Medical Science, "Federico II" University of Naples, Naples, Italy
| | - Federico Pietrocola
- Equipe 11 labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; Institut National de la Santé et de la Recherche Médicale, UMR1138, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Université Pierre et Marie Curie, Paris, France; Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Claudia Einer
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine Borchard
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andree Zibert
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Münster, Germany
| | - Hartmut H Schmidt
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Münster, Germany
| | | | | | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Translational Medical Science, "Federico II" University of Naples, Naples, Italy
| | - Guido Kroemer
- Equipe 11 labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; Institut National de la Santé et de la Recherche Médicale, UMR1138, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Université Pierre et Marie Curie, Paris, France; Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Toxicology and Environmental Hygiene, Technical University Munich, Munich, Germany
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.
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Eremina L, Pashintseva N, Kovalev L, Kovaleva M, Shishkin S. Proteomics of mammalian mitochondria in health and malignancy: From protein identification to function. Anal Biochem 2018; 552:4-18. [DOI: 10.1016/j.ab.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
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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: 23] [Impact Index Per Article: 2.9] [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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Tharkeshwar AK, Gevaert K, Annaert W. Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell. Proteomics 2017; 18:e1700113. [PMID: 29125683 DOI: 10.1002/pmic.201700113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022]
Abstract
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyzing changes in the composition of these compartments. Reduction of the biomolecular complexity of a sample helps to identify low abundant molecules, but such a reductionist approach requires methods that enable proper isolation and purification of individual cellular organelles. Decades of research have led to the development of a plethora of isolation methods for a broad range of subcellular organelles; yet, in particular, intrinsically dynamic compartments belonging to the endocytic machinery, including the plasma membrane, remain difficult to isolate in a sufficiently pure fraction. In this review, we discuss various methods that are commonly used to isolate subcellular organelles from cells and evaluate their advantages and disadvantages.
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Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Cell Biology, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium
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Kayo S, Bahnemann J, Klauser M, Pörtner R, Zeng AP. A microfluidic device for immuno-affinity-based separation of mitochondria from cell culture. LAB ON A CHIP 2013; 13:4467-75. [PMID: 24084793 DOI: 10.1039/c3lc50739d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this work, we present a method to isolate mitochondria of mammalian cells after cell disruption on microscale. The device is composed of linear microchannels cast in PDMS (polydimethylsiloxane). Specific antibodies against the translocase outer membrane protein of the mitochondria are immobilized on the surface of the substrate using an avidin-biotin sandwich construct. The mitochondria can be captured in the channel, whereas the remains of the cell lysate flow out the chip unhindered. The captured mitochondria can be observed directly on chip. A successful immobilization of pre-isolated mitochondria was shown at a flow rate between 0 and 5 μl min(-1) (≈0-2.5 mm s(-1)). After fluorescence staining, we demonstrated that the mitochondria covered around 3% of the channel surface. The mitochondria appeared in a distinct spherical shape with a diameter of around 0.8-1.2 μm. Further validation of the microfluidic device using non-treated cell lysate was done at 2 μl min(-1). The immobilized mitochondria were smaller with a diameter of around ≈490 nm. We observed a surface coverage of around 4%. The immobilized mitochondria were active and stable for over 2 h without cooling and were shown to be able to produce ATP under stage 3 respiration on chip.
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Affiliation(s)
- Sabrina Kayo
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestraße 15, 21075 Hamburg, Germany.
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9
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Schulz S, Schmitt S, Wimmer R, Aichler M, Eisenhofer S, Lichtmannegger J, Eberhagen C, Artmann R, Tookos F, Walch A, Krappmann D, Brenner C, Rust C, Zischka H. Progressive stages of mitochondrial destruction caused by cell toxic bile salts. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2121-33. [PMID: 23685124 DOI: 10.1016/j.bbamem.2013.05.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/26/2013] [Accepted: 05/07/2013] [Indexed: 11/19/2022]
Abstract
The cell-toxic bile salt glycochenodeoxycholic acid (GCDCA) and taurochenodeoxycholic acid (TCDCA) are responsible for hepatocyte demise in cholestatic liver diseases, while tauroursodeoxycholic acid (TUDCA) is regarded hepatoprotective. We demonstrate the direct mitochondrio-toxicity of bile salts which deplete the mitochondrial membrane potential and induce the mitochondrial permeability transition (MPT). The bile salt mediated mechanistic mode of destruction significantly differs from that of calcium, the prototype MPT inducer. Cell-toxic bile salts initially bind to the mitochondrial outer membrane. Subsequently, the structure of the inner boundary membrane disintegrates. And it is only thereafter that the MPT is induced. This progressive destruction occurs in a dose- and time-dependent way. We demonstrate that GCDCA and TCDCA, but not TUDCA, preferentially permeabilize liposomes containing the mitochondrial membrane protein ANT, a process resembling the MPT induction in whole mitochondria. This suggests that ANT is one decisive target for toxic bile salts. To our knowledge this is the first report unraveling the consecutive steps leading to mitochondrial destruction by cell-toxic bile salts.
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Affiliation(s)
- Sabine Schulz
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
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10
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Zischka H, Lichtmannegger J, Schmitt S, Jägemann N, Schulz S, Wartini D, Jennen L, Rust C, Larochette N, Galluzzi L, Chajes V, Bandow N, Gilles VS, DiSpirito AA, Esposito I, Goettlicher M, Summer KH, Kroemer G. Liver mitochondrial membrane crosslinking and destruction in a rat model of Wilson disease. J Clin Invest 2011; 121:1508-18. [PMID: 21364284 PMCID: PMC3068979 DOI: 10.1172/jci45401] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 01/05/2011] [Indexed: 11/17/2022] Open
Abstract
Wilson disease (WD) is a rare hereditary condition that is caused by a genetic defect in the copper-transporting ATPase ATP7B that results in hepatic copper accumulation and lethal liver failure. The present study focuses on the structural mitochondrial alterations that precede clinical symptoms in the livers of rats lacking Atp7b, an animal model for WD. Liver mitochondria from these Atp7b–/– rats contained enlarged cristae and widened intermembrane spaces, which coincided with a massive mitochondrial accumulation of copper. These changes, however, preceded detectable deficits in oxidative phosphorylation and biochemical signs of oxidative damage, suggesting that the ultrastructural modifications were not the result of oxidative stress imposed by copper- dependent Fenton chemistry. In a cell-free system containing a reducing dithiol agent, isolated mitochondria exposed to copper underwent modifications that were closely related to those observed in vivo. In this cell-free system, copper induced thiol modifications of three abundant mitochondrial membrane proteins, and this correlated with reversible intramitochondrial membrane crosslinking, which was also observed in liver mitochondria from Atp7b–/– rats. In vivo, copper-chelating agents reversed mitochondrial accumulation of copper, as well as signs of intra-mitochondrial membrane crosslinking, thereby preserving the functional and structural integrity of mitochondria. Together, these findings suggest that the mitochondrion constitutes a pivotal target of copper in WD.
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Affiliation(s)
- Hans Zischka
- Institute of Toxicology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.
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Trost M, Bridon G, Desjardins M, Thibault P. Subcellular phosphoproteomics. MASS SPECTROMETRY REVIEWS 2010; 29:962-90. [PMID: 20931658 DOI: 10.1002/mas.20297] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Protein phosphorylation represents one of the most extensively studied post-translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification both in vitro and in vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein-protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post-translational modifications. While numerous large-scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio-temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation.
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Affiliation(s)
- Matthias Trost
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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Moschallski M, Hausmann M, Posch A, Paulus A, Kunz N, Duong TT, Angres B, Fuchsberger K, Steuer H, Stoll D, Werner S, Hagmeyer B, Stelzle M. MicroPrep: Chip-based dielectrophoretic purification of mitochondria. Electrophoresis 2010; 31:2655-63. [DOI: 10.1002/elps.201000097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Wen J, Wilker EW, Yaffe MB, Jensen KF. Microfluidic preparative free-flow isoelectric focusing: system optimization for protein complex separation. Anal Chem 2010; 82:1253-60. [PMID: 20092256 DOI: 10.1021/ac902157e] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isoelectric focusing (IEF) is the first step for two-dimensional (2D) gel electrophoresis and plays an important role in sample purification for proteomics. However, biases in protein size and pI resolution, as well as limitations in sample volume, gel capacity, sample loss, and experimental time, remain challenges. In order to address some of the limitations of traditional IEF, we present a microfluidic free flow IEF (FF-IEF) device for continuous protein separation into 24 fractions. The device reproducibly establishes a nearly linear pH gradient from 4 to 10. Optimized dynamic coatings of 4% poly(vinyl alcohol) (PVA) minimize peak broadening by transverse electrokinetic flows. Even though the device operates at high electric fields (up to 370 V/cm), efficient cooling maintains solution temperature inside the separation channel controllably in the range 2-25 degrees C. Protein samples with a dynamic concentration range from microg/mL to mg/mL can be loaded into the microdevice at a flow rate of 1 mL/h and residence time of approximately 12 min. By using a protein complex of nine proteins and 13 isoforms, we demonstrate improved separation with the FF-IEF system over traditional 2D gel electrophoresis. Device-to-device reproducibility is also illustrated through the efficient depletion of the albumin and hemoglobin assays. Post-device sample concentrations result in a 10-20-fold increase, which allow for isolation and detection of low abundance proteins. The separation of specific proteins from a whole cell lysate is demonstrated as an example. The microdevice has the further benefits of retaining high molecular weight proteins, providing higher yield of protein that has a broader range in pI, and reducing experimental time compared to conventional IEF IGP gel strip approaches.
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Affiliation(s)
- Jian Wen
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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14
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Abstract
Contamination from subcellular organelles and myelin has hindered attempts to characterize the lipidome of brain mitochondria. A high degree of mitochondrial purity is required for accurate measurements of the content and molecular species composition of mitochondrial lipids. We devised a discontinuous Ficoll and sucrose gradient procedure for the isolation and purification of brain mitochondria free from any detectable contamination. Shotgun lipidomics was used to analyze the lipid composition of the brain mitochondria. These procedures can be used to determine whether intrinsic lipid abnormalities underlie mitochondrial dysfunction associated with neurological and neurodegenerative diseases.
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15
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Chaiyarit S, Thongboonkerd V. Comparative analyses of cell disruption methods for mitochondrial isolation in high-throughput proteomics study. Anal Biochem 2009; 394:249-58. [DOI: 10.1016/j.ab.2009.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 07/14/2009] [Accepted: 07/17/2009] [Indexed: 01/30/2023]
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Gauthier DJ, Lazure C. Complementary methods to assist subcellular fractionation in organellar proteomics. Expert Rev Proteomics 2008; 5:603-17. [PMID: 18761470 DOI: 10.1586/14789450.5.4.603] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Organellar proteomics aims to describe the full complement of proteins of subcellular structures and organelles. When compared with whole-cell or whole-tissue proteomes, the more focused results from subcellular proteomic studies have yielded relatively simpler datasets from which biologically relevant information can be more easily extracted. In every proteomic study, the quality and purity of the biological sample to be investigated is of the utmost importance for a successful analysis. In organellar proteomics, one of the most crucial steps in sample preparation is the initial subcellular fractionation procedure by which the enriched preparation of the sought-after organelle is obtained. In nearly all available organellar proteomic studies, the method of choice relies on one or several rounds of density-based gradient centrifugation. Although this method has been recognized for decades as yielding relatively pure preparations of organelles, recent technological advances in protein separation and identification can now reveal even minute amounts of contamination, which in turn can greatly complicate data interpretation. The scope of this review focuses on recently published innovative complementary or alternative methods to perform subcellular fractionation, which can further refine the way in which sample preparation is accomplished in organellar proteomics.
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Affiliation(s)
- Daniel J Gauthier
- Neuropeptides Structure and Metabolism Research Unit, Institut de Recherches Cliniques de Montréal, University of Montréal, 110 Pine Avenue West, Montréal, Québec, Canada H2W 1R7.
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