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Janero DR. Current strategic trends in drug discovery: the present as prologue. Expert Opin Drug Discov 2024; 19:147-159. [PMID: 37936504 DOI: 10.1080/17460441.2023.2275640] [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: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION Escalating costs and inherent uncertainties associated with drug discovery invite initiatives to improve its efficiency and de-risk campaigns for inventing better therapeutics. One such initiative involves recognizing and exploiting current approaches in therapeutics invention with molecular mechanisms of action that hold promise for designing and targeting new chemical entities as drugs. AREAS COVERED This perspective considers the current contextual framework around three drug-discovery approaches and evaluates their potential to help identify new targets/modalities in small-molecule molecular pharmacology: diversifying ligand-directed phenotypes for G protein-coupled receptor (GPCR) pharmacotherapeutic signaling; developing therapeutic-protein degraders and stabilizers for proximity-inducing pharmacology; and mining organelle biology for druggable therapeutic targets. EXPERT OPINION The contemporary drug-discovery approaches examined appear generalizable and versatile to have applications in therapeutics invention beyond those case studies discussed herein. Accordingly, they may be considered strategic trends worthy of note in advancing the field toward novel ways of addressing pharmacotherapeutically unmet medical needs.
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Affiliation(s)
- David R Janero
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, and Health Sciences Entrepreneurs, Northeastern University, Boston, MA, USA
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2
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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3
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Ahmad F, Ramamorthy S, Areeshi MY, Ashraf GM, Haque S. Isolated Mitochondrial Preparations and In organello Assays: A Powerful and Relevant Ex vivo Tool for Assessment of Brain (Patho)physiology. Curr Neuropharmacol 2023; 21:1433-1449. [PMID: 36872352 PMCID: PMC10324330 DOI: 10.2174/1570159x21666230303123555] [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: 05/16/2022] [Revised: 10/30/2022] [Accepted: 12/29/2022] [Indexed: 03/07/2023] Open
Abstract
Mitochondria regulate multiple aspects of neuronal development, physiology, plasticity, and pathology through their regulatory roles in bioenergetic, calcium, redox, and cell survival/death signalling. While several reviews have addressed these different aspects, a comprehensive discussion focussing on the relevance of isolated brain mitochondria and their utilities in neuroscience research has been lacking. This is relevant because the employment of isolated mitochondria rather than their in situ functional evaluation, offers definitive evidence of organelle-specificity, negating the interference from extra mitochondrial cellular factors/signals. This mini-review was designed primarily to explore the commonly employed in organello analytical assays for the assessment of mitochondrial physiology and its dysfunction, with a particular focus on neuroscience research. The authors briefly discuss the methodologies for biochemical isolation of mitochondria, their quality assessment, and cryopreservation. Further, the review attempts to accumulate the key biochemical protocols for in organello assessment of a multitude of mitochondrial functions critical for neurophysiology, including assays for bioenergetic activity, calcium and redox homeostasis, and mitochondrial protein translation. The purpose of this review is not to examine each and every method or study related to the functional assessment of isolated brain mitochondria, but rather to assemble the commonly used protocols of in organello mitochondrial research in a single publication. The hope is that this review will provide a suitable platform aiding neuroscientists to choose and apply the required protocols and tools to address their particular mechanistic, diagnostic, or therapeutic question dealing within the confines of the research area of mitochondrial patho-physiology in the neuronal perspective.
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Affiliation(s)
- Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, 632014, India
| | - Siva Ramamorthy
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, 632014, India
| | - Mohammed Y. Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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4
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Fu A. Mitotherapy as a Novel Therapeutic Strategy for Mitochondrial Diseases. Curr Mol Pharmacol 2021; 13:41-49. [PMID: 31345157 DOI: 10.2174/1874467212666190920144115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/07/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The mitochondrion is a multi-functional organelle that is mainly responsible for energy supply in the mammalian cells. Over 100 human diseases are attributed to mitochondrial dysfunction. Mitochondrial therapy (mitotherapy) aims to transfer functional exogenous mitochondria into mitochondria-defective cells for recovery of the cell viability and consequently, prevention of the disease progress. OBJECTIVE The review summarizes the evidence on exogenous mitochondria that can directly enter mammalian cells for disease therapy following local and intravenous administration, and suggests that when healthy cells donate their mitochondria to damaged cells, the mitochondrial transfer between cells serve as a new mode of cell rescue. Then the transferred mitochondria play their roles in recipient cells, including energy production and maintenance of cell function. CONCLUSION Mitotherapy makes the of modulation of cell survival possible, and it would be a potential therapeutic strategy for mitochondrial diseases.
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Affiliation(s)
- Ailing Fu
- School of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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5
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Li N, Zhan X. MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS. MASS SPECTROMETRY REVIEWS 2020; 39:471-498. [PMID: 32020673 DOI: 10.1002/mas.21618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
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6
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Pyrethroid exposure and neurotoxicity: a mechanistic approach. Arh Hig Rada Toksikol 2019; 70:74-89. [DOI: 10.2478/aiht-2019-70-3263] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/01/2019] [Indexed: 12/27/2022] Open
Abstract
Abstract
Pyrethroids are a class of synthetic insecticides that are used widely in and around households to control the pest. Concerns about exposure to this group of pesticides are now mainly related to their neurotoxicity and nigrostriatal dopaminergic neurodegeneration seen in Parkinson’s disease. The main neurotoxic mechanisms include oxidative stress, inflammation, neuronal cell loss, and mitochondrial dysfunction. The main neurodegeneration targets are ion channels. However, other receptors, enzymes, and several signalling pathways can also participate in disorders induced by pyrethroids. The aim of this review is to elucidate the main mechanisms involved in neurotoxicity caused by pyrethroids deltamethrin, permethrin, and cypermethrin. We also review common targets and pathways of Parkinson’s disease therapy, including Nrf2, Nurr1, and PPARγ, and how they are affected by exposure to pyrethroids. We conclude with possibilities to be addressed by future research of novel methods of protection against neurological disorders caused by pesticides that may also find their use in the management/treatment of Parkinson’s disease.
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Bons J, Macron C, Aude-Garcia C, Vaca-Jacome SA, Rompais M, Cianférani S, Carapito C, Rabilloud T. A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level. Mol Cell Proteomics 2019; 18:1085-1095. [PMID: 31154437 PMCID: PMC6553941 DOI: 10.1074/mcp.ra118.001269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coupled with the cleavage of a presequence called the transit peptide, and the formation of a new N-terminus. Determination of the neo N-termini has been investigated by proteomic approaches in several systems, but generally in a static way to compile as many N-termini as possible. In the present study, we have investigated how the mitochondrial proteome and N-terminome react to chemical stimuli that alter mitochondrial metabolism, namely zinc ions and rapamycin. To this end, we have used a strategy that analyzes both internal and N-terminal peptides in a single run, the dN-TOP approach. We used these two very different stressors to sort out what could be a generic response to stress and what is specific to each of these stressors. Rapamycin and zinc induced different changes in the mitochondrial proteome. However, convergent changes to key mitochondrial enzymatic activities such as pyruvate dehydrogenase, succinate dehydrogenase and citrate synthase were observed for both treatments. Other convergent changes were seen in components of the N-terminal processing system and mitochondrial proteases. Investigations into the generation of neo-N-termini in mitochondria showed that the processing system is robust, as indicated by the lack of change in neo N-termini under the conditions tested. Detailed analysis of the data revealed that zinc caused a slight reduction in the efficiency of the N-terminal trimming system and that both treatments increased the degradation of mitochondrial proteins. In conclusion, the use of this combined strategy allowed a detailed analysis of the dynamics of the mitochondrial N-terminome in response to treatments which impact the mitochondria.
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Affiliation(s)
- Joanna Bons
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Charlotte Macron
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Catherine Aude-Garcia
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
| | - Sebastian Alvaro Vaca-Jacome
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Magali Rompais
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Christine Carapito
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France;
| | - Thierry Rabilloud
- §Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, BIG-LCBM, 38000 Grenoble, France
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8
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Wolters JC, Permentier HP, Bakker BM, Bischoff R. Targeted Proteomics to Study Mitochondrial Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:101-117. [PMID: 31452138 DOI: 10.1007/978-981-13-8367-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Targeted mass spectrometry in the selected or parallel reaction monitoring (SRM or PRM) mode is a widely used methodology to quantify proteins based on so-called signature or proteotypic peptides. SRM has the advantage of being able to quantify a range of proteins in a single analysis, for example, to measure the level of enzymes comprising a biochemical pathway. In this chapter, we will detail how to set up an SRM assay on the example of the mitochondrial protein succinate dehydrogenase [ubiquinone] flavoprotein subunit (mouse UniProt-code Q8K2B3). First, we will outline the in silico assay design including the choice of peptides based on a range of properties. We will further delineate different quantification strategies and introduce the reader to LC-MS assay development including the selection of the optimal peptide charge state and fragment ions as well as a discussion of the dynamic range of detection. The chapter will close with an application from the area of mitochondrial biology related to the quantification of a set of proteins isolated from mouse liver mitochondria in a study on mitochondrial respiratory flux decline in aging mouse muscle.
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Affiliation(s)
- Justina C Wolters
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
- Laboratory of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
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Kume K, Amagasa T, Hashimoto T, Kitagawa H. NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms. Evol Bioinform Online 2018; 14:1176934318819835. [PMID: 30626996 PMCID: PMC6305954 DOI: 10.1177/1176934318819835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023] Open
Abstract
To estimate the functions of mitochondria of diverse eukaryotic nonmodel organisms in which the mitochondrial proteomes are not available, it is necessary to predict the protein sequence features of the mitochondrial proteins computationally. Various prediction methods that are trained using the proteins of model organisms belonging particularly to animals, plants, and fungi exist. However, such methods may not be suitable for predicting the proteins derived from nonmodel organisms because the sequence features of the mitochondrial proteins of diversified nonmodel organisms can differ from those of model organisms that are present only in restricted parts of the tree of eukaryotes. Here, we proposed NommPred, which predicts the mitochondrial proteins of nonmodel organisms that are widely distributed over eukaryotes. We used a gradient boosting machine to develop 2 predictors-one for predicting the proteins of mitochondria and the other for predicting the proteins of mitochondrion-related organelles that are highly reduced mitochondria. The performance of both predictors was found to be better than that of the best method available.
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Affiliation(s)
- Keitaro Kume
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Toshiyuki Amagasa
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroyuki Kitagawa
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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10
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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11
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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: 0.5] [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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12
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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13
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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14
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Jin K, Musso G, Vlasblom J, Jessulat M, Deineko V, Negroni J, Mosca R, Malty R, Nguyen-Tran DH, Aoki H, Minic Z, Freywald T, Phanse S, Xiang Q, Freywald A, Aloy P, Zhang Z, Babu M. Yeast Mitochondrial Protein–Protein Interactions Reveal Diverse Complexes and Disease-Relevant Functional Relationships. J Proteome Res 2015; 14:1220-37. [DOI: 10.1021/pr501148q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ke Jin
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Gabriel Musso
- Cardiovascular
Division, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - James Vlasblom
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Matthew Jessulat
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Viktor Deineko
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Jacopo Negroni
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
| | - Roberto Mosca
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
| | - Ramy Malty
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Diem-Hang Nguyen-Tran
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zoran Minic
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Tanya Freywald
- Cancer Research
Unit, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Sadhna Phanse
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Qian Xiang
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Freywald
- Cancer Research
Unit, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Patrick Aloy
- Joint
IRB−BSC Program in Computational Biology, IRB, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Zhaolei Zhang
- Terrence
Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Mohan Babu
- Department
of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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15
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Chen X, Cui Z, Wei S, Hou J, Xie Z, Peng X, Li J, Cai T, Hang H, Yang F. Chronic high glucose induced INS-1β cell mitochondrial dysfunction: a comparative mitochondrial proteome with SILAC. Proteomics 2014; 13:3030-9. [PMID: 23956156 DOI: 10.1002/pmic.201200448] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 06/28/2013] [Accepted: 07/23/2013] [Indexed: 11/08/2022]
Abstract
As glucose-stimulated insulin secretion of pancreatic β cell is triggered and promoted by the metabolic messengers derived from mitochondria, mitochondria take a central stage in the normal function of β cells. β cells in diabetics were chronically exposed to hyperglycemia stimulation, which have been reported to exert deleterious effects on β-cell mitochondria. However, the mechanism of the toxic effects of hyperglycemia on β-cell mitochondria was not clear. In this study, we characterized the biological functional changes of rat INS-1β cells and their mitochondria with chronic exposure to hyperglycemia and created a research model of chronic hyperglycemia-induced dysfunctional β cells with damaged mitochondria. Then, SILAC-based quantitative proteomic approach was used to compare the mitochondrial protein expression from high glucose treated INS-1β cells and control cells. The expression of some mitochondrial proteins was found with significant changes. Functional classification revealed most of these proteins were related with oxidative phosphorylation, mitochondrial protein biosynthesis, substances metabolism, transport, and cell death. These results presented some useful information about the effect of glucotoxicity on the β-cell mitochondria.
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Affiliation(s)
- Xiulan Chen
- Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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16
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Agrawal S, Singh A, Tripathi P, Mishra M, Singh PK, Singh MP. Cypermethrin-Induced Nigrostriatal Dopaminergic Neurodegeneration Alters the Mitochondrial Function:A Proteomics Study. Mol Neurobiol 2014; 51:448-65. [DOI: 10.1007/s12035-014-8696-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/24/2014] [Indexed: 12/29/2022]
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17
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Panis C. Unraveling Oxidation-Induced Modifications in Proteins by Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:19-38. [DOI: 10.1016/b978-0-12-800168-4.00002-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Vlasblom J, Jin K, Kassir S, Babu M. Exploring mitochondrial system properties of neurodegenerative diseases through interactome mapping. J Proteomics 2013; 100:8-24. [PMID: 24262152 DOI: 10.1016/j.jprot.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/08/2013] [Accepted: 11/06/2013] [Indexed: 12/20/2022]
Abstract
UNLABELLED Mitochondria are double membraned, dynamic organelles that are required for a large number of cellular processes, and defects in their function have emerged as causative factors for a growing number of human disorders and are highly associated with cancer, metabolic, and neurodegenerative (ND) diseases. Biochemical and genetic investigations have uncovered small numbers of candidate mitochondrial proteins (MPs) involved in ND disease, but given the diversity of processes affected by MP function and the difficulty of detecting interactions involving these proteins, many more likely remain unknown. However, high-throughput proteomic and genomic approaches developed in genetically tractable model prokaryotes and lower eukaryotes have proven to be effective tools for querying the physical (protein-protein) and functional (gene-gene) relationships between diverse types of proteins, including cytosolic and membrane proteins. In this review, we highlight how experimental and computational approaches developed recently by our group and others can be effectively used towards elucidating the mitochondrial interactome in an unbiased and systematic manner to uncover network-based connections. We discuss how the knowledge from the resulting interaction networks can effectively contribute towards the identification of new mitochondrial disease gene candidates, and thus further clarify the role of mitochondrial biology and the complex etiologies of ND disease. BIOLOGICAL SIGNIFICANCE Biochemical and genetic investigations have uncovered small numbers of candidate mitochondrial proteins (MPs) involved in neurodegenerative (ND) diseases, but given the diversity of processes affected by MP function and the difficulty of detecting interactions involving these proteins, many more likely remain unknown. Large-scale proteomic and genomic approaches developed in model prokaryotes and lower eukaryotes have proven to be effective tools for querying the physical (protein-protein) and functional (gene-gene) relationships between diverse types of proteins. Extension of this new framework to the mitochondrial sub-system in human will likewise provide a universally informative systems-level view of the physical and functional landscape for exploring the evolutionary principles underlying mitochondrial function. In this review, we highlight how experimental and computational approaches developed recently by our group and others can be effectively used towards elucidating the mitochondrial interactome in an unbiased and systematic manner to uncover network-based connections. We anticipate that the knowledge from these resulting interaction networks can effectively contribute towards the identification of new mitochondrial disease gene candidates, and thus foster a deeper molecular understanding of mitochondrial biology as well as the etiology of mitochondrial diseases. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- James Vlasblom
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ke Jin
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Sandy Kassir
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada.
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19
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Warda M, Kim HK, Kim N, Ko KS, Rhee BD, Han J. A matter of life, death and diseases: mitochondria from a proteomic perspective. Expert Rev Proteomics 2013; 10:97-111. [PMID: 23414362 DOI: 10.1586/epr.12.69] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mitochondria are highly ordered, integrated organelles that energize cellular activities and contribute to programmed death by initiating disciplined apoptotic cascades. This review seeks to clarify our understanding of mitochondrial structural-functional integrity beyond the resolved nuclear genome by unraveling the dynamic mitochondrial proteome and elucidating proteome/genome interplay. The roles of mechanochemical coupling between mitoskeleton and cytoskeleton and crosstalk with other organelles in orchestrating cellular outcomes are explained. The authors also review the modulation of mitochondrial-related oxidative stress on apoptosis and cancer development and the context is applied to interpret pathogenetic events in neurodegenerative disorders and cardiovascular diseases. The accumulated proteomics evidence is used to describe the integral role that mitochondria play and how they influence other intracellular organelles. Possible mitochondrial-targeted therapeutic interventions are also discussed.
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Affiliation(s)
- Mohamad Warda
- Biochemistry, Molecular Biology and Chemistry of Nutrition Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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20
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Abstract
Mitochondria have an essential role in powering cells by generating ATP following the metabolism of pyruvate derived from glycolysis. They are also the major source of generating reactive oxygen species (ROS), which have regulatory roles in cell death and proliferation. Mutations in mitochondrial DNA (mtDNA) and dysregulation of mitochondrial metabolism have been frequently described in human tumors. Although the role of oxidative stress as the consequence of mtDNA mutations and/or altered mitochondrial functions has been demonstrated in carciongenesis, a causative role of mitochondria in tumor progression has only been demonstrated recently. Specifically, the subject of this mini-review focuses on the role of mitochondria in promoting cancer metastasis. Cancer relapse and the subsequent spreading of cancer cells to distal sites are leading causes of morbidity and mortality in cancer patients. Despite its clinical importance, the underlying mechanisms of metastasis remain to be elucidated. Recently, it was demonstrated that mitochondrial oxidative stress could actively promote tumor progression and increase the metastatic potential of cancer cells. The purpose of this mini-review is to summarize current investigations of the roles of mitochondria in cancer metastasis. Future development of diagnostic and therapeutic strategies for patients with advanced cancer will benefit from the new knowledge of mitochondrial metabolism in epithelial cancer cells and the tumor stroma.
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Affiliation(s)
- Emily I Chen
- Department Of Pharmacological Sciences & Proteomics Center School Of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA.
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21
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An iTRAQ-based mitoproteomics approach for profiling the nephrotoxicity mechanisms of ochratoxin A in HEK 293 cells. J Proteomics 2013; 78:398-415. [DOI: 10.1016/j.jprot.2012.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/28/2012] [Accepted: 10/11/2012] [Indexed: 01/05/2023]
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22
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Messana I, Cabras T, Iavarone F, Vincenzoni F, Urbani A, Castagnola M. Unraveling the different proteomic platforms. J Sep Sci 2012; 36:128-39. [PMID: 23212829 DOI: 10.1002/jssc.201200830] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 01/06/2023]
Abstract
This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.
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Affiliation(s)
- Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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23
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Gregersen N, Hansen J, Palmfeldt J. Mitochondrial proteomics--a tool for the study of metabolic disorders. J Inherit Metab Dis 2012; 35:715-26. [PMID: 22526845 DOI: 10.1007/s10545-012-9480-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 12/14/2022]
Abstract
Mitochondria are important for a number of life and death processes, such as energy production, creation of reactive oxygen species, and elicitation of stress responses. These responses range from induction of protein quality control and antioxidant systems to mitochondria elimination and cell death. Mitochondrial dysfunctions are involved in pathologies associated with many diseases, for example metabolic disorders, diabetes, cancers, cardiovascular and neurodegenerative diseases as well as obesity and aging. Mitochondrial proteomics can be a powerful tool in the study of these diseases, especially since it can cover mitochondrial proteins from several metabolic pathways, such as the citric acid cycle, fatty acid oxidation, and respiratory chain, as well as protein networks involved in stress responses. The mitochondrial proteome can consist of more than 1,000 different proteins. However, it is difficult to define the precise number, since mitochondria are dynamic and difficult to purify, and because an unknown number of proteins possess dual or multiple localization, depending on cell type and physiological conditions. This review describes several quantitative studies of proteins from mitochondria isolated by centrifugation, separated by various methods (e.g., electrophoresis and nanoLC), and analyzed by advanced mass spectrometry. We illustrate the methods by showing that multiple pathways and networks are affected in cells from patients carrying gene variations affecting a mitochondrial protein. The study of cultured skin fibroblasts from patients with ethylmalonic aciduria associated with variations in the genes coding for short-chain acyl-CoA dehydrogenase (SCAD) or ETHE1 are two of the examples. The possibility of obtaining mitochondrial proteomics data from whole cell proteomics studies is also exemplified by the involvement of liver mitochondria in metabolic syndrome.
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Affiliation(s)
- Niels Gregersen
- Research Unit for Molecular Medicine, Institute of Clinical Medicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
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24
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Anand R, Langer T, Baker MJ. Proteolytic control of mitochondrial function and morphogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:195-204. [PMID: 22749882 DOI: 10.1016/j.bbamcr.2012.06.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 06/08/2012] [Accepted: 06/15/2012] [Indexed: 12/18/2022]
Abstract
Mitochondrial proteostasis depends on a hierarchical system of tightly controlled quality surveillance mechanisms. Proteases within mitochondria take center stage in this network. They eliminate misfolded and damaged proteins and ensure the biogenesis and morphogenesis of mitochondria by processing or degrading short-lived regulatory proteins. Mitochondrial gene expression, the mitochondrial phospholipid metabolism and the fusion of mitochondrial membranes are under proteolytic control. Furthermore, in response to stress and mitochondrial dysfunction, proteolysis inhibits fusion and facilitates mitophagy and apoptosis. Defining these versatile activities of mitochondrial proteases will be pivotal for understanding the pathogenesis of various neurodegenerative disorders associated with defective mitochondria-associated proteolysis. This article is part of a Special Issue entitled: Mitochondrial dynamics and physiology.
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25
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Vishal C, Kumar JU, Veera Brahmendra Swamy C, Nandini R, Srinivas G, Kumaresan R, Shashi S, Sreedhar AS. Repercussion of Mitochondria Deformity Induced by Anti-Hsp90 Drug 17AAG in Human Tumor Cells. Drug Target Insights 2011; 5:11-32. [PMID: 22087060 PMCID: PMC3178438 DOI: 10.4137/dti.s6582] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Inhibiting Hsp90 chaperone roles using 17AAG induces cytostasis or apoptosis in tumor cells through destabilization of several mutated cancer promoting proteins. Although mitochondria are central in deciding the fate of cells, 17AAG induced effects on tumor cell mitochondria were largely unknown. Here, we show that Hsp90 inhibition with 17AAG first affects mitochondrial integrity in different human tumor cells, neuroblastoma, cervical cancer and glial cells. Using human neuroblastoma tumor cells, we found the early effects associated with a change in mitochondrial membrane potential, elongation and engorgement of mitochondria because of an increased matrix vacuolization. These effects are specific to Hsp90 inhibition as other chemotherapeutic drugs did not induce similar mitochondrial deformity. Further, the effects are independent of oxidative damage and cytoarchitecture destabilization since cytoskeletal disruptors and mitochondrial metabolic inhibitors also do not induce similar deformity induced by 17AAG. The 1D PAGE LC MS/MS mitochondrial proteome analysis of 17AAG treated human neuroblastoma cells showed a loss of 61% proteins from membrane, metabolic, chaperone and ribonucleoprotein families. About 31 unmapped protein IDs were identified from proteolytic processing map using Swiss-Prot accession number, and converted to the matching gene name searching the ExPASy proteomics server. Our studies display that Hsp90 inhibition effects at first embark on mitochondria of tumor cells and compromise mitochondrial integrity.
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Affiliation(s)
- Chaturvedi Vishal
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, Uppal Road, India
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26
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Staunton L, O'Connell K, Ohlendieck K. Proteomic Profiling of Mitochondrial Enzymes during Skeletal Muscle Aging. J Aging Res 2011; 2011:908035. [PMID: 21437005 PMCID: PMC3062155 DOI: 10.4061/2011/908035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/17/2010] [Accepted: 01/03/2011] [Indexed: 11/20/2022] Open
Abstract
Mitochondria are of central importance for energy generation in skeletal muscles. Expression changes or functional alterations in mitochondrial enzymes play a key role during myogenesis, fibre maturation, and various neuromuscular pathologies, as well as natural fibre aging. Mass spectrometry-based proteomics suggests itself as a convenient large-scale and high-throughput approach to catalogue the mitochondrial protein complement and determine global changes during health and disease. This paper gives a brief overview of the relatively new field of mitochondrial proteomics and discusses the findings from recent proteomic surveys of mitochondrial elements in aged skeletal muscles. Changes in the abundance, biochemical activity, subcellular localization, and/or posttranslational modifications in key mitochondrial enzymes might be useful as novel biomarkers of aging. In the long term, this may advance diagnostic procedures, improve the monitoring of disease progression, help in the testing of side effects due to new drug regimes, and enhance our molecular understanding of age-related muscle degeneration.
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Affiliation(s)
- Lisa Staunton
- Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
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27
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Ohlendieck K. Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques. Skelet Muscle 2011; 1:6. [PMID: 21798084 PMCID: PMC3143904 DOI: 10.1186/2044-5040-1-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 02/01/2011] [Indexed: 01/08/2023] Open
Abstract
Background Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes. Results Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins. Conclusions This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.
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Affiliation(s)
- Kay Ohlendieck
- Muscle Biology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.
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