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Das J, Bhattacharjee S, Saha S. mitoPADdb: A database of mitochondrial proteins associated with diseases. Mitochondrion 2024; 78:101927. [PMID: 38944368 DOI: 10.1016/j.mito.2024.101927] [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: 03/08/2024] [Revised: 06/04/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Mitochondrial protein/gene mutations and expression variations contribute to the pathogenesis of various diseases, such as neurodegenerative and metabolic diseases. Detailed studies on mitochondrial protein-encoding (MPE) genes across diseases can provide clues for novel therapeutic strategies. Here, we collected, compiled, and manually curated the MPE gene mutation and expression variations data and their association with diseases in a single platform named mitoPADdb. The database contains 810 genes with 18,356 mutations and 1284 qualitative expression variations associated with 1793 diseases, grouped into 15 categories. It allows users to perform a comparative quantitative gene expression analysis for 317 transcriptomic studies across disease categories. Further, it provides information on MPE genes-associated molecular pathways. The mitoPADdb is a valuable resource for investigating mitochondrial dysfunction-related diseases. It can be accessed via http://bicresources.jcbose.ac.in/ssaha4/mitopaddb/index.html.
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Affiliation(s)
- Jagannath Das
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India
| | - Sudipto Bhattacharjee
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, 700098, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India.
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2
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Arkat S, Poovitha S, Vijayakumar A, Dhat R, Sitasawad SL, Mahapatra NR. Regulation of peroxiredoxin-3 gene expression under basal and hyperglycemic conditions: Key roles for transcription factors Sp1, CREB and NF-κB. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166691. [PMID: 36933848 DOI: 10.1016/j.bbadis.2023.166691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/27/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
Peroxiredoxin-3 (Prx-3), a thioredoxin-dependent peroxidase located exclusively in the mitochondrial matrix, catalyses peroxides/peroxinitrites. Altered levels of Prx-3 is associated with diabetic cardiomyopathy (DCM). However, molecular mechanisms of Prx-3 gene regulation remain partially understood. We undertook a systemic analysis of the Prx-3 gene to identify the key motifs and transcriptional regulatory molecules. Transfection of promoter-reporter constructs in the cultured cells identified -191/+20 bp domain as the core promoter region. Stringent in silico analysis of this core promoter revealed putative binding sites for specificity protein 1 (Sp1), cAMP response element-binding protein (CREB) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Interestingly, while co-transfection of the -191/+20 bp construct with Sp1/CREB plasmid diminished Prx3 promoter-reporter activity, mRNA and protein levels, co-transfection with NF-κB expression plasmid augmented the same. Consistently, inhibition of Sp1/CREB/NF-κB expression reversed the promoter-reporter activity, mRNA and protein levels of Prx-3, thereby confirming their regulatory effects. ChIP assays provided evidence for interactions of Sp1/CREB/NF-κB with the Prx-3 promoter. H9c2 cells treated with high glucose as well as streptozotocin (STZ)-treated diabetic rats showed time-dependent reduction in promoter activity, endogenous transcript and protein levels of Prx-3. Augmentation of Sp1/CREB protein levels and their strong binding with Prx-3 promoter are responsible for diminished Prx-3 levels under hyperglycemia. The activation/increase in the NF-κB expression under hyperglycemia was not sufficient to restore the reduction of endogenous Prx-3 levels owing to its weak binding affinity. Taken together, this study elucidates the previously unknown roles of Sp1/CREB/NF-κB in regulating Prx-3 gene expression under hyperglycemic condition.
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Affiliation(s)
- Silpa Arkat
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sundar Poovitha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Anupama Vijayakumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Rohini Dhat
- National Centre for Cell Science, NCCS Complex, S.P. Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Sandhya L Sitasawad
- National Centre for Cell Science, NCCS Complex, S.P. Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Proteomics as a Tool for the Study of Mitochondrial Proteome, Its Dysfunctionality and Pathological Consequences in Cardiovascular Diseases. Int J Mol Sci 2023; 24:ijms24054692. [PMID: 36902123 PMCID: PMC10003354 DOI: 10.3390/ijms24054692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
The focus of this review is on the proteomic approaches applied to the study of the qualitative/quantitative changes in mitochondrial proteins that are related to impaired mitochondrial function and consequently different types of pathologies. Proteomic techniques developed in recent years have created a powerful tool for the characterization of both static and dynamic proteomes. They can detect protein-protein interactions and a broad repertoire of post-translation modifications that play pivotal roles in mitochondrial regulation, maintenance and proper function. Based on accumulated proteomic data, conclusions can be derived on how to proceed in disease prevention and treatment. In addition, this article will present an overview of the recently published proteomic papers that deal with the regulatory roles of post-translational modifications of mitochondrial proteins and specifically with cardiovascular diseases connected to mitochondrial dysfunction.
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Ranjbarvaziri S, Kooiker KB, Ellenberger M, Fajardo G, Zhao M, Vander Roest AS, Woldeyes RA, Koyano TT, Fong R, Ma N, Tian L, Traber GM, Chan F, Perrino J, Reddy S, Chiu W, Wu JC, Woo JY, Ruppel KM, Spudich JA, Snyder MP, Contrepois K, Bernstein D. Altered Cardiac Energetics and Mitochondrial Dysfunction in Hypertrophic Cardiomyopathy. Circulation 2021; 144:1714-1731. [PMID: 34672721 PMCID: PMC8608736 DOI: 10.1161/circulationaha.121.053575] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/24/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure-function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. In this work, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM. METHODS We performed a comprehensive multiomics profile of the molecular (transcripts, metabolites, and complex lipids), ultrastructural, and functional components of HCM energetics using myocardial samples from 27 HCM patients and 13 normal controls (donor hearts). RESULTS Integrated omics analysis revealed alterations in a wide array of biochemical pathways with major dysregulation in fatty acid metabolism, reduction of acylcarnitines, and accumulation of free fatty acids. HCM hearts showed evidence of global energetic decompensation manifested by a decrease in high energy phosphate metabolites (ATP, ADP, and phosphocreatine) and a reduction in mitochondrial genes involved in creatine kinase and ATP synthesis. Accompanying these metabolic derangements, electron microscopy showed an increased fraction of severely damaged mitochondria with reduced cristae density, coinciding with reduced citrate synthase activity and mitochondrial oxidative respiration. These mitochondrial abnormalities were associated with elevated reactive oxygen species and reduced antioxidant defenses. However, despite significant mitochondrial injury, HCM hearts failed to upregulate mitophagic clearance. CONCLUSIONS Overall, our findings suggest that perturbed metabolic signaling and mitochondrial dysfunction are common pathogenic mechanisms in patients with HCM. These results highlight potential new drug targets for attenuation of the clinical disease through improving metabolic function and reducing mitochondrial injury.
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Affiliation(s)
- Sara Ranjbarvaziri
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kristina B. Kooiker
- Department of Medicine, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - Mathew Ellenberger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanni Fajardo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingming Zhao
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alison Schroer Vander Roest
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Robyn Fong
- Department of Cardiothoracic Surgery, Stanford University, CA, USA
| | - Ning Ma
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiology, Stanford University, Stanford, CA, USA
| | - Lei Tian
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiology, Stanford University, Stanford, CA, USA
| | - Gavin M. Traber
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Frandics Chan
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - John Perrino
- Cell Sciences Imaging Facility, Stanford University, Stanford, CA, USA
| | - Sushma Reddy
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Joseph C. Wu
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiology, Stanford University, Stanford, CA, USA
| | - Joseph Y. Woo
- Department of Cardiothoracic Surgery, Stanford University, CA, USA
| | - Kathleen M. Ruppel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, USA
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Andreadou I, Efentakis P, Frenis K, Daiber A, Schulz R. Thiol-based redox-active proteins as cardioprotective therapeutic agents in cardiovascular diseases. Basic Res Cardiol 2021; 116:44. [PMID: 34275052 DOI: 10.1007/s00395-021-00885-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
Thiol-based redox compounds, namely thioredoxins (Trxs), glutaredoxins (Grxs) and peroxiredoxins (Prxs), stand as a pivotal group of proteins involved in antioxidant processes and redox signaling. Glutaredoxins (Grxs) are considered as one of the major families of proteins involved in redox regulation by removal of S-glutathionylation and thereby reactivation of other enzymes with thiol-dependent activity. Grxs are also coupled to Trxs and Prxs recycling and thereby indirectly contribute to reactive oxygen species (ROS) detoxification. Peroxiredoxins (Prxs) are a ubiquitous family of peroxidases, which play an essential role in the detoxification of hydrogen peroxide, aliphatic and aromatic hydroperoxides, and peroxynitrite. The Trxs, Grxs and Prxs systems, which reversibly induce thiol modifications, regulate redox signaling involved in various biological events in the cardiovascular system. This review focuses on the current knowledge of the role of Trxs, Grxs and Prxs on cardiovascular pathologies and especially in cardiac hypertrophy, ischemia/reperfusion (I/R) injury and heart failure as well as in the presence of cardiovascular risk factors, such as hypertension, hyperlipidemia, hyperglycemia and metabolic syndrome. Further studies on the roles of thiol-dependent redox systems in the cardiovascular system will support the development of novel protective and therapeutic strategies against cardiovascular diseases.
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Affiliation(s)
- Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece.
| | - Panagiotis Efentakis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Katie Frenis
- Department of Cardiology 1, Molecular Cardiology, University Medical Center of the Johannes Gutenberg University, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Andreas Daiber
- Department of Cardiology 1, Molecular Cardiology, University Medical Center of the Johannes Gutenberg University, Langenbeckstr. 1, 55131, Mainz, Germany.,Partner Site Rhine-Main, German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University Giessen, Giessen, Germany.
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Moro L. The Mitochondrial Proteome of Tumor Cells: A SnapShot on Methodological Approaches and New Biomarkers. BIOLOGY 2020; 9:biology9120479. [PMID: 33353059 PMCID: PMC7766083 DOI: 10.3390/biology9120479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Simple Summary Mitochondria are central hubs of cellular signaling, energy metabolism, and redox balance. The plasticity of these cellular organelles is an essential requisite for the cells to cope with different stimuli and stress conditions. Cancer cells are characterized by changes in energy metabolism, mitochondrial signaling, and dynamics. These changes are driven by alterations in the mitochondrial proteome. For this reason, in the last years a focus of basic and cancer research has been the implementation and optimization of technologies to investigate changes in the mitochondrial proteome during cancer initiation and progression. This review presents an overview of the most used technologies to investigate the mitochondrial proteome and recent evidence on changes in the expression levels and delocalization of certain proteins in and out the mitochondria for shaping the functional properties of tumor cells. Abstract Mitochondria are highly dynamic and regulated organelles implicated in a variety of important functions in the cell, including energy production, fatty acid metabolism, iron homeostasis, programmed cell death, and cell signaling. Changes in mitochondrial metabolism, signaling and dynamics are hallmarks of cancer. Understanding whether these modifications are associated with alterations of the mitochondrial proteome is particularly relevant from a translational point of view because it may contribute to better understanding the molecular bases of cancer development and progression and may provide new potential prognostic and diagnostic biomarkers as well as novel molecular targets for anti-cancer treatment. Making an inventory of the mitochondrial proteins has been particularly challenging given that there is no unique consensus targeting sequence that directs protein import into mitochondria, some proteins are present at very low levels, while other proteins are expressed only in some cell types, in a particular developmental stage or under specific stress conditions. This review aims at providing the state-of-the-art on methodologies used to characterize the mitochondrial proteome in tumors and highlighting the biological relevance of changes in expression and delocalization of proteins in and out the mitochondria in cancer biology.
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Affiliation(s)
- Loredana Moro
- Institute of Biomembranes, Bioenergetic and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70125 Bari, Italy
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Kruse R, Sahebekhtiari N, Højlund K. The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance. Int J Mol Sci 2020; 21:ijms21155374. [PMID: 32731645 PMCID: PMC7432338 DOI: 10.3390/ijms21155374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the currently available studies characterizing the mitochondrial proteome in human skeletal muscle in insulin-resistant conditions, such as obesity, T2D, and aging, as well as exercise-mediated changes in the mitochondrial proteome. Furthermore, we outline technical challenges and limitations and methodological aspects that should be considered when planning future large-scale proteomics studies of mitochondria from human skeletal muscle. Authors’ view: At present, most proteomic studies of skeletal muscle or isolated muscle mitochondria have demonstrated a reduced abundance of proteins in several mitochondrial biological processes in obesity, T2D, and aging, whereas the beneficial effects of exercise involve an increased content of muscle proteins involved in mitochondrial metabolism. Powerful mass-spectrometry-based proteomics now provides unprecedented opportunities to perform in-depth proteomics of muscle mitochondria, which in the near future is expected to increase our understanding of the complex molecular mechanisms underlying the link between mitochondrial dysfunction and insulin resistance in chronic metabolic disorders.
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Affiliation(s)
- Rikke Kruse
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Navid Sahebekhtiari
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
- Correspondence: ; Tel.: +45-2532-06-48
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Abstract
Atrial fibrillation (AF), the most common progressive and age-related cardiac arrhythmia, affects millions of people worldwide. AF is associated with common risk factors, including hypertension, diabetes mellitus, and obesity, and serious complications such as stroke and heart failure. Notably, AF is progressive in nature, and because current treatment options are mainly symptomatic, they have only a moderate effect on prevention of arrhythmia progression. Hereto, there is an urgent unmet need to develop mechanistic treatments directed at root causes of AF. Recent research findings indicate a key role for inflammasomes and derailed proteostasis as root causes of AF. Here, we elaborate on the molecular mechanisms of these 2 emerging key pathways driving the pathogenesis of AF. First the role of NLRP3 (NACHT, LRR, and PYD domains-containing protein 3) inflammasome on AF pathogenesis and cardiomyocyte remodeling is discussed. Then we highlight pathways of proteostasis derailment, including exhaustion of cardioprotective heat shock proteins, disruption of cytoskeletal proteins via histone deacetylases, and the recently discovered DNA damage-induced nicotinamide adenine dinucleotide+ depletion to underlie AF. Moreover, potential interactions between the inflammasomes and proteostasis pathways are discussed and possible therapeutic targets within these pathways indicated.
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Affiliation(s)
- Na Li
- From the Department of Medicine (Cardiovascular Research) (N.L.), Baylor College of Medicine, Houston, TX.,Department of Molecular Physiology and Biophysics (N.L.), Baylor College of Medicine, Houston, TX.,Cardiovascular Research Institute (N.L.), Baylor College of Medicine, Houston, TX
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam UMC, Vrije Universiteit, Amsterdam Cardiovascular Sciences, the Netherlands (B.J.J.M.B.)
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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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10
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Sharapov MG, Fesenko EE, Novoselov VI. The Role of Peroxiredoxins in Various Diseases Caused by Oxidative Stress and the Prospects of Using Exogenous Peroxiredoxins. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918040164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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11
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Serum proteome profiling in canine idiopathic dilated cardiomyopathy using TMT-based quantitative proteomics approach. J Proteomics 2018. [PMID: 29530679 DOI: 10.1016/j.jprot.2018.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins. To complement the proteomic analysis, serum biochemical parameters and levels of know biomarkers of cardiac function were measured. Several proteins with biomarker potential were identified, such as inter-alpha-trypsin inhibitor heavy chain H4, microfibril-associated glycoprotein 4 and apolipoprotein A-IV, which were validated using an independent method (Western blotting) and showed high specificity and sensitivity according to the receiver operating characteristic curve analysis. Bioinformatics analysis revealed involvement of different pathways in iDCM, such as complement cascade activation, lipoprotein particles dynamics, elastic fibre formation, GPCR signalling and respiratory electron transport chain. SIGNIFICANCE Idiopathic dilated cardiomyopathy is a severe primary myocardial disease of unknown cause, affecting both humans and dogs. This study is a contribution to the canine heart disease research by means of proteomic and bioinformatic state of the art analyses, following similar approach in human iDCM research. Importantly, we used serum as non-invasive and easily accessible biological source of information and contributed to the scarce data on biofluid proteome research on this topic. Bioinformatics analysis revealed biological pathways modulated in canine iDCM with potential of further targeted research. Also, several proteins with biomarker potential have been identified and successfully validated.
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12
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Abstract
The incidence and prevalence of cardiac diseases, which are the main cause of death worldwide, are likely to increase because of population ageing. Prevailing theories about the mechanisms of ageing feature the gradual derailment of cellular protein homeostasis (proteostasis) and loss of protein quality control as central factors. In the heart, loss of protein patency, owing to flaws in genetically-determined design or because of environmentally-induced 'wear and tear', can overwhelm protein quality control, thereby triggering derailment of proteostasis and contributing to cardiac ageing. Failure of protein quality control involves impairment of chaperones, ubiquitin-proteosomal systems, autophagy, and loss of sarcomeric and cytoskeletal proteins, all of which relate to induction of cardiomyocyte senescence. Targeting protein quality control to maintain cardiac proteostasis offers a novel therapeutic strategy to promote cardiac health and combat cardiac disease. Currently marketed drugs are available to explore this concept in the clinical setting.
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Affiliation(s)
- Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, De Boelelaan 1117, 1081 HZ Amsterdam, The Netherlands
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13
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McDermott-Roe C, Leleu M, Rowe GC, Palygin O, Bukowy JD, Kuo J, Rech M, Hermans-Beijnsberger S, Schaefer S, Adami E, Creemers EE, Heinig M, Schroen B, Arany Z, Petretto E, Geurts AM. Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PLoS One 2017; 12:e0170458. [PMID: 28158196 PMCID: PMC5291451 DOI: 10.1371/journal.pone.0170458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/05/2017] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein. To focus the analysis on a medically-important condition with a strong yet incompletely understood mitochondrial component, candidates were cross-referenced with an MPET-enriched module independently generated via genome-wide co-expression network analysis of a human heart failure gene expression dataset. The strongest uncharacterized candidate in the analysis was Leucine Rich Repeat Containing 2 (LRRC2). LRRC2 was found to be localized to the mitochondria in human cells and transcriptionally-regulated by the mitochondrial master regulator Pgc-1α. We report that Lrrc2 transcript abundance correlates with that of β-MHC, a canonical marker of cardiac hypertrophy in humans and experimentally demonstrated an elevation in Lrrc2 transcript in in vitro and in vivo rodent models of cardiac hypertrophy as well as in patients with dilated cardiomyopathy. RNAi-mediated Lrrc2 knockdown in a rat-derived cardiomyocyte cell line resulted in enhanced expression of canonical hypertrophic biomarkers as well as increased mitochondrial mass in the context of increased Pgc-1α expression. In conclusion, our meta-analysis represents a simple yet powerful springboard for the nomination of putative mitochondrially-pertinent proteins relevant to cardiac function and enabled the identification of LRRC2 as a novel mitochondrially-relevant protein and regulator of the hypertrophic response.
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Affiliation(s)
- Chris McDermott-Roe
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Glenn C. Rowe
- Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Oleg Palygin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - John D. Bukowy
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Judy Kuo
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Monika Rech
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Steffie Hermans-Beijnsberger
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Sebastian Schaefer
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Esther E. Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Aron M. Geurts
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
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14
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Toczek M, Zielonka D, Zukowska P, Marcinkowski JT, Slominska E, Isalan M, Smolenski RT, Mielcarek M. An impaired metabolism of nucleotides underpins a novel mechanism of cardiac remodeling leading to Huntington's disease related cardiomyopathy. Biochim Biophys Acta Mol Basis Dis 2016; 1862:2147-2157. [PMID: 27568644 DOI: 10.1016/j.bbadis.2016.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/04/2016] [Accepted: 08/23/2016] [Indexed: 01/28/2023]
Abstract
Huntington's disease (HD) is mainly thought of as a neurological disease, but multiple epidemiological studies have demonstrated a number of cardiovascular events leading to heart failure in HD patients. Our recent studies showed an increased risk of heart contractile dysfunction and dilated cardiomyopathy in HD pre-clinical models. This could potentially involve metabolic remodeling, that is a typical feature of the failing heart, with reduced activities of high energy phosphate generating pathways. In this study, we sought to identify metabolic abnormalities leading to HD-related cardiomyopathy in pre-clinical and clinical settings. We found that HD mouse models developed a profound deterioration in cardiac energy equilibrium, despite AMP-activated protein kinase hyperphosphorylation. This was accompanied by a reduced glucose usage and a significant deregulation of genes involved in de novo purine biosynthesis, in conversion of adenine nucleotides, and in adenosine metabolism. Consequently, we observed increased levels of nucleotide catabolites such as inosine, hypoxanthine, xanthine and uric acid, in murine and human HD serum. These effects may be caused locally by mutant HTT, via gain or loss of function effects, or distally by a lack of trophic signals from central nerve stimulation. Either may lead to energy equilibrium imbalances in cardiac cells, with activation of nucleotide catabolism plus an inhibition of re-synthesis. Our study suggests that future therapies should target cardiac mitochondrial dysfunction to ameliorate energetic dysfunction. Importantly, we describe the first set of biomarkers related to heart and skeletal muscle dysfunction in both pre-clinical and clinical HD settings.
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Affiliation(s)
- Marta Toczek
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki Str, 80-210 Gdansk, Poland
| | - Daniel Zielonka
- Department of Social Medicine, Poznan University of Medical Sciences, 6 Rokietnicka Str, 60-806 Poznan, Poland
| | - Paulina Zukowska
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki Str, 80-210 Gdansk, Poland
| | - Jerzy T Marcinkowski
- Department of Social Medicine, Poznan University of Medical Sciences, 6 Rokietnicka Str, 60-806 Poznan, Poland
| | - Ewa Slominska
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki Str, 80-210 Gdansk, Poland
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, Exhibition Road, SW7 2AZ London, UK
| | - Ryszard T Smolenski
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki Str, 80-210 Gdansk, Poland.
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, Exhibition Road, SW7 2AZ London, UK.
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15
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Proteomics of human mitochondria. Mitochondrion 2016; 33:2-14. [PMID: 27444749 DOI: 10.1016/j.mito.2016.07.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 12/25/2022]
Abstract
Proteomics have passed through a tremendous development in the recent years by the development of ever more sensitive, fast and precise mass spectrometry methods. The dramatically increased research in the biology of mitochondria and their prominent involvement in all kinds of diseases and ageing has benefitted from mitochondrial proteomics. We here review substantial findings and progress of proteomic analyses of human cells and tissues in the recent past. One challenge for investigations of human samples is the ethically and medically founded limited access to human material. The increased sensitivity of mass spectrometry technology aids in lowering this hurdle and new approaches like generation of induced pluripotent cells from somatic cells allow to produce patient-specific cellular disease models with great potential. We describe which human sample types are accessible, review the status of the catalog of human mitochondrial proteins and discuss proteins with dual localization in mitochondria and other cellular compartments. We describe the status and developments of pertinent mass spectrometric strategies, and the use of databases and bioinformatics. Using selected illustrative examples, we draw a picture of the role of proteomic analyses for the many disease contexts from inherited disorders caused by mutation in mitochondrial proteins to complex diseases like cancer, type 2 diabetes and neurodegenerative diseases. Finally, we speculate on the future role of proteomics in research on human mitochondria and pinpoint fields where the evolving technologies will be exploited.
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16
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Ortega A, Tarazón E, Roselló-Lletí E, Gil-Cayuela C, Lago F, González-Juanatey JR, Cinca J, Jorge E, Martínez-Dolz L, Portolés M, Rivera M. Patients with Dilated Cardiomyopathy and Sustained Monomorphic Ventricular Tachycardia Show Up-Regulation of KCNN3 and KCNJ2 Genes and CACNG8-Linked Left Ventricular Dysfunction. PLoS One 2015; 10:e0145518. [PMID: 26710323 PMCID: PMC4692400 DOI: 10.1371/journal.pone.0145518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/05/2015] [Indexed: 01/26/2023] Open
Abstract
AIMS Disruptions in cardiac ion channels have shown to influence the impaired cardiac contraction in heart failure. We sought to determine the altered gene expression profile of this category in dilated cardiomyopathy (DCM) patients and relate the altered gene expression with the clinical signs present in our patients, such as ventricular dysfunction and sustained monomorphic ventricular tachycardia (SMVT). METHODS AND RESULTS Left ventricular (LV) tissue samples were used in RNA-sequencing technique to elucidate the transcriptomic changes of 13 DCM patients compared to controls (n = 10). We analyzed the differential gene expression of cardiac ion channels, and we found a total of 34 altered genes. We found that the calcium channel CACNG8 mRNA and protein levels were down-regulated and highly and inversely related with LV ejection fraction (LVEF) (r = -0.78, P<0.01). Furthermore, the potassium channels KCNN3 and KCNJ2 mRNA and protein levels were up-regulated and showed also a significant and inverse correlation with LVEF (r = -0.61, P<0.05; r = -0.60, P<0.05) in patients with SMVT. CONCLUSION A broad set of deregulated genes have been identified by RNA-sequencing technique. The relationship of CACNG8, KCNN3 and KCNJ2 with LVEF, and the up-regulation of KCNN3 and KCNJ2 in all patients with SMVT, irrespective of CACNG8 expression, suggest a significant role for these three ion flux related genes in the LV dysfunction present in this cardiomyopathy and an important relationship between KCNN3 and KCNJ2 up-regulation and the presence of SMVT.
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Affiliation(s)
- Ana Ortega
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
| | - Estefanía Tarazón
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
| | - Esther Roselló-Lletí
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
| | - Carolina Gil-Cayuela
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
| | - Francisca Lago
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - Jose-Ramón González-Juanatey
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - Juan Cinca
- Cardiology Service of Santa Creu i Sant Pau Hospital, Barcelona, Spain
| | - Esther Jorge
- Cardiology Service of Santa Creu i Sant Pau Hospital, Barcelona, Spain
| | - Luis Martínez-Dolz
- Heart Failure and Transplantation Unit, Cardiology Department, La Fe University Hospital, Valencia, Spain
| | - Manuel Portolés
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
| | - Miguel Rivera
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain
- * E-mail:
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