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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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Mota GAF, de Souza SLB, Vileigas DF, da Silva VL, Sant'Ana PG, Costa LCDS, Padovani CR, Zanatti Bazan SG, Buzalaf MAR, Santos LDD, Okoshi MP, Gatto M, Cicogna AC. Myocardial proteome changes in aortic stenosis rats subjected to long-term aerobic exercise. J Cell Physiol 2024; 239:e31199. [PMID: 38291668 DOI: 10.1002/jcp.31199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
The effects of exercise training (ET) on the heart of aortic stenosis (AS) rats are controversial and the mechanisms involved in alterations induced by ET have been poorly clarified. In this study, we analyzed the myocardial proteome to identify proteins modulated by moderate-intensity aerobic ET in rats with chronic supravalvular AS. Wistar rats were divided into four groups: sedentary control (C-Sed), exercised control (C-Ex), sedentary aortic stenosis (AS-Sed), and exercised AS (AS-Ex). ET consisted of five treadmill running sessions per week for 16 weeks. Statistical analysis was performed by ANOVA or Kruskal-Wallis and Goodman tests. Results were discussed at a significance level of 5%. At the end of the experiment, AS-Ex rats had higher functional capacity, lower blood lactate concentration, and better cardiac structural and left ventricular (LV) functional parameters than the AS-Sed. Myocardial proteome analysis showed that AS-Sed had higher relative protein abundance related to the glycolytic pathway, oxidative stress, and inflammation, and lower relative protein abundance related to beta-oxidation than C-Sed. AS-Ex had higher abundance of one protein related to mitochondrial biogenesis and lower relative protein abundance associated with oxidative stress and inflammation than AS-Sed. Proteomic data were validated for proteins related to lipid and glycolytic metabolism. Chronic pressure overload changes the abundance of myocardial proteins that are mainly involved in lipid and glycolytic energy metabolism in rats. Moderate-intensity aerobic training attenuates changes in proteins related to oxidative stress and inflammation and increases the COX4I1 protein, related to mitochondrial biogenesis. Protein changes are combined with improved functional capacity, cardiac remodeling, and LV function in AS rats.
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Affiliation(s)
- Gustavo Augusto Ferreira Mota
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Sérgio Luiz Borges de Souza
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | | | - Vitor Loureiro da Silva
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Paula Grippa Sant'Ana
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Licia Carla da Silva Costa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, São Paulo, Brazil
| | - Carlos Roberto Padovani
- Department of Biostatistics, Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Silméia Garcia Zanatti Bazan
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | | | | | - Marina Politi Okoshi
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Mariana Gatto
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Antonio Carlos Cicogna
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
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Cockova Z, Ujcikova H, Telensky P, Novotny J. Protein profiling of SH-SY5Y neuroblastoma cells: The effect of rhein. J Biosci 2019. [DOI: 10.1007/s12038-019-9908-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Delles C, Carrick E, Graham D, Nicklin SA. Utilizing proteomics to understand and define hypertension: where are we and where do we go? Expert Rev Proteomics 2018; 15:581-592. [PMID: 29999442 PMCID: PMC6092739 DOI: 10.1080/14789450.2018.1493927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Hypertension is a complex and multifactorial cardiovascular disorder. With different mechanisms contributing to a different extent to an individual's blood pressure, the discovery of novel pathogenetic principles of hypertension is challenging. However, there is an urgent and unmet clinical need to improve prevention, detection, and therapy of hypertension in order to reduce the global burden associated with hypertension-related cardiovascular diseases. Areas covered: Proteomic techniques have been applied in reductionist experimental models including angiotensin II infusion models in rodents and the spontaneously hypertensive rat in order to unravel mechanisms involved in blood pressure control and end organ damage. In humans proteomic studies mainly focus on prediction and detection of organ damage, particularly of heart failure and renal disease. While there are only few proteomic studies specifically addressing human primary hypertension, there are more data available in hypertensive disorders in pregnancy, such as preeclampsia. We will review these studies and discuss implications of proteomics on precision medicine approaches. Expert commentary: Despite the potential of proteomic studies in hypertension there has been moderate progress in this area of research. Standardized large-scale studies are required in order to make best use of the potential that proteomics offers in hypertension and other cardiovascular diseases.
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Affiliation(s)
- Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Emma Carrick
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Delyth Graham
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Stuart A. Nicklin
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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Changes in the activity of some metabolic enzymes in the heart of SHR rat incurred by transgenic expression of CD36. J Physiol Biochem 2018; 74:479-489. [PMID: 29916179 DOI: 10.1007/s13105-018-0641-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/12/2018] [Indexed: 01/12/2023]
Abstract
Hypertension, dyslipidemia, and insulin resistance in the spontaneously hypertensive rat (SHR) can be alleviated by rescuing CD36 fatty acid translocase. The present study investigated whether transgenic rescue of CD36 in SHR could affect mitochondrial function and activity of selected metabolic enzymes in the heart. These analyses were conducted on ventricular preparations derived from SHR and from transgenic strain SHR-Cd36 that expresses a functional wild-type CD36. Our respirometric measurements revealed that mitochondria isolated from the left ventricles exhibited two times higher respiratory activity than those isolated from the right ventricles. Whereas, we did not observe any significant changes in functioning of the mitochondrial respiratory system between both rat strains, enzyme activities of total hexokinase, and both mitochondrial and total malate dehydrogenase were markedly decreased in the left ventricles of transgenic rats, compared to SHR. We also detected downregulated expression of the succinate dehydrogenase subunit SdhB (complex II) and 70 kDa peroxisomal membrane protein in the left ventricles of SHR-Cd36. These data indicate that CD36 may affect in a unique fashion metabolic substrate flexibility of the left and right ventricles.
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Kuda O, Brezinova M, Silhavy J, Landa V, Zidek V, Dodia C, Kreuchwig F, Vrbacky M, Balas L, Durand T, Hübner N, Fisher AB, Kopecky J, Pravenec M. Nrf2-Mediated Antioxidant Defense and Peroxiredoxin 6 Are Linked to Biosynthesis of Palmitic Acid Ester of 9-Hydroxystearic Acid. Diabetes 2018; 67:1190-1199. [PMID: 29549163 PMCID: PMC6463562 DOI: 10.2337/db17-1087] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are lipid mediators with promising antidiabetic and anti-inflammatory properties that are formed in white adipose tissue (WAT) via de novo lipogenesis, but their biosynthetic enzymes are unknown. Using a combination of lipidomics in WAT, quantitative trait locus mapping, and correlation analyses in rat BXH/HXB recombinant inbred strains, as well as response to oxidative stress in murine models, we elucidated the potential pathway of biosynthesis of several FAHFAs. Comprehensive analysis of WAT samples identified ∼160 regioisomers, documenting the complexity of this lipid class. The linkage analysis highlighted several members of the nuclear factor, erythroid 2 like 2 (Nrf2)-mediated antioxidant defense system (Prdx6, Mgst1, Mgst3), lipid-handling proteins (Cd36, Scd6, Acnat1, Acnat2, Baat), and the family of flavin containing monooxygenases (Fmo) as the positional candidate genes. Transgenic expression of Nrf2 and deletion of Prdx6 genes resulted in reduction of palmitic acid ester of 9-hydroxystearic acid (9-PAHSA) and 11-PAHSA levels, while oxidative stress induced by an inhibitor of glutathione synthesis increased PAHSA levels nonspecifically. Our results indicate that the synthesis of FAHFAs via carbohydrate-responsive element-binding protein-driven de novo lipogenesis depends on the adaptive antioxidant system and suggest that FAHFAs may link activity of this system with insulin sensitivity in peripheral tissues.
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Affiliation(s)
- Ondrej Kuda
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Marie Brezinova
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Silhavy
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Landa
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vaclav Zidek
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Chandra Dodia
- Institute for Environmental Medicine and Department of Physiology, University of Pennsylvania, Philadelphia, PA
| | - Franziska Kreuchwig
- Max Delbrück Center for Molecular Medicine, German Centre for Cardiovascular Research, and Charité - Universitätsmedizin, Berlin, Germany
| | - Marek Vrbacky
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Laurence Balas
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université Montpellier, ENSCM, Faculté de Pharmacie, Montpellier, France
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, German Centre for Cardiovascular Research, and Charité - Universitätsmedizin, Berlin, Germany
| | - Aron B Fisher
- Institute for Environmental Medicine and Department of Physiology, University of Pennsylvania, Philadelphia, PA
| | - Jan Kopecky
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
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Eckhardt A, Kulhava L, Miksik I, Pataridis S, Hlavackova M, Vasinova J, Kolar F, Sedmera D, Ostadal B. Proteomic analysis of cardiac ventricles: baso-apical differences. Mol Cell Biochem 2018; 445:211-219. [PMID: 29302836 DOI: 10.1007/s11010-017-3266-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/23/2017] [Indexed: 12/19/2022]
Abstract
The heart is characterized by a remarkable degree of heterogeneity. Since different cardiac pathologies affect different cardiac regions, it is important to understand molecular mechanisms by which these parts respond to pathological stimuli. In addition to already described left ventricular (LV)/right ventricular (RV) and transmural differences, possible baso-apical heterogeneity has to be taken into consideration. The aim of our study has been, therefore, to compare proteomes in the apical and basal parts of the rat RV and LV. Two-dimensional electrophoresis was used for the proteomic analysis. The major result of this study has revealed for the first time significant baso-apical differences in concentration of several proteins, both in the LV and RV. As far as the LV is concerned, five proteins had higher concentration in the apical compared to basal part of the ventricle. Three of them are mitochondrial and belong to the "metabolism and energy pathways" (myofibrillar creatine kinase M-type, L-lactate dehydrogenase, dihydrolipoamide dehydrogenase). Myosin light chain 3 is a contractile protein and HSP60 belongs to heat shock proteins. In the RV, higher concentration in the apical part was observed in two mitochondrial proteins (creatine kinase S-type and proton pumping NADH:ubiquinone oxidoreductase). The described changes were more pronounced in the LV, which is subjected to higher workload. However, in both chambers was the concentration of proteins markedly higher in the apical than that in basal part, which corresponds to the higher energetic demand and contractile activity of these segments of both ventricles.
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Affiliation(s)
- Adam Eckhardt
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.
| | - Lucie Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague, Czech Republic
| | - Ivan Miksik
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Statis Pataridis
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Marketa Hlavackova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Physiology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Jana Vasinova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Frantisek Kolar
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - David Sedmera
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Kateřinská 32, Prague, Czech Republic
| | - Bohuslav Ostadal
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
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Sugiyama Y, Kameshita I. Multi-PK antibodies: Powerful analytical tools to explore the protein kinase world. Biochem Biophys Rep 2017; 11:40-45. [PMID: 28955766 PMCID: PMC5614692 DOI: 10.1016/j.bbrep.2017.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/07/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Diverse biological events are regulated through protein phosphorylation mediated by protein kinases. Some of these protein kinases are known to be involved in the pathogenesis of various diseases. Although 518 protein kinase genes were identified in the human genome, it remains unclear how many and what kind of protein kinases are expressed and activated in cells and tissues under varying situations. To investigate cellular signaling by protein kinases, we developed monoclonal antibodies, designated as Multi-PK antibodies, that can recognize multiple protein kinases in various biological species. These Multi-PK antibodies can be used to profile the kinases expressed in cells and tissues, identify the kinases of special interest, and analyze protein kinase expression and phosphorylation state. Here we introduce some applications of Multi-PK antibodies to identify and characterize the protein kinases involved in epigenetics, glucotoxicity in type 2 diabetes, and pathogenesis of ulcerative colitis. In this review, we focus on the recently developed technologies for kinomics studies using the powerful analytical tools of Multi-PK antibodies. Multi-PK antibodies recognize a wide variety of protein kinases. New analytical methods using Multi-PK antibodies for protein kinase studies are explained. Kinomics studies using Multi-PK antibodies are introduced.
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Key Words
- 2D-PAGE, two-dimensional polyacrylamide gel electrophoresis
- CDKL5, cyclin-dependent kinase-like 5
- CNBr, cyanogen bromide
- CaMK, Ca2+/calmodulin-dependent protein kinase
- DCLK, double-cortin like protein kinase
- Dnmt1, DNA methyltransferase 1
- FAK, focal adhesion kinase
- IEF, isoelectric focusing
- IPG, immobilized pH gradient
- Kinomics
- MAPK, mitogen-activated protein kinase
- MeCP2, methylated-CpG-binding protein 2
- Monoclonal antibody
- Protein kinase
- Protein phosphorylation
- Proteomics
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El Rassi Z, Puangpila C. Liquid-phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2014-2016. Electrophoresis 2016; 38:150-161. [DOI: 10.1002/elps.201600413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Ziad El Rassi
- Department of Chemistry; Oklahoma State University; Stillwater OK USA
| | - Chanida Puangpila
- Department of Chemistry, Faculty of Science; Chiang Mai University; Chiang Mai Thailand
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