1
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Wang J, Zhu X, Wang S, Zhang Y, Hua W, Liu Z, Zheng Y, Lu X. Phosphoproteomic and proteomic profiling in post-infarction chronic heart failure. Front Pharmacol 2023; 14:1181622. [PMID: 37405054 PMCID: PMC10315476 DOI: 10.3389/fphar.2023.1181622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Background: Post-infarction chronic heart failure is the most common type of heart failure. Patients with chronic heart failure show elevated morbidity and mortality with limited evidence-based therapies. Phosphoproteomic and proteomic analysis can provide insights regarding molecular mechanisms underlying post-infarction chronic heart failure and explore new therapeutic approaches. Methods and results: Global quantitative phosphoproteomic and proteomic analysis of left ventricular tissues from post-infarction chronic heart failure rats were performed. A total of 33 differentially expressed phosphorylated proteins (DPPs) and 129 differentially expressed proteins were identified. Bioinformatic analysis indicated that DPPs were enriched mostly in nucleocytoplasmic transport and mRNA surveillance pathway. Bclaf1 Ser658 was identified after construction of Protein-Protein Interaction Network and intersection with Thanatos Apoptosis Database. Predicted Upstream Kinases of DPPs based on kinase-substrate enrichment analysis (KSEA) app showed 13 kinases enhanced in heart failure. Proteomic analysis showed marked changes in protein expression related to cardiac contractility and metabolism. Conclusion: The present study marked phosphoproteomics and proteomics changes in post-infarction chronic heart failure. Bclaf1 Ser658 might play a critical role in apoptosis in heart failure. PRKAA1, PRKACA, and PAK1 might serve as potential therapeutic targets for post-infarction chronic heart failure.
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Affiliation(s)
| | | | | | | | | | | | - Yu Zheng
- *Correspondence: Yu Zheng, ; Xiao Lu,
| | - Xiao Lu
- *Correspondence: Yu Zheng, ; Xiao Lu,
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2
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Valero-Muñoz M, Saw EL, Hekman RM, Blum BC, Hourani Z, Granzier H, Emili A, Sam F. Proteomic and phosphoproteomic profiling in heart failure with preserved ejection fraction (HFpEF). Front Cardiovasc Med 2022; 9:966968. [PMID: 36093146 PMCID: PMC9452734 DOI: 10.3389/fcvm.2022.966968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Although the prevalence of heart failure with preserved ejection fraction (HFpEF) is increasing, evidence-based therapies for HFpEF remain limited, likely due to an incomplete understanding of this disease. This study sought to identify the cardiac-specific features of protein and phosphoprotein changes in a murine model of HFpEF using mass spectrometry. HFpEF mice demonstrated moderate hypertension, left ventricle (LV) hypertrophy, lung congestion and diastolic dysfunction. Proteomics analysis of the LV tissue showed that 897 proteins were differentially expressed between HFpEF and Sham mice. We observed abundant changes in sarcomeric proteins, mitochondrial-related proteins, and NAD-dependent protein deacetylase sirtuin-3 (SIRT3). Upregulated pathways by GSEA analysis were related to immune modulation and muscle contraction, while downregulated pathways were predominantly related to mitochondrial metabolism. Western blot analysis validated SIRT3 downregulated cardiac expression in HFpEF vs. Sham (0.8 ± 0.0 vs. 1.0 ± 0.0; P < 0.001). Phosphoproteomics analysis showed that 72 phosphosites were differentially regulated between HFpEF and Sham LV. Aberrant phosphorylation patterns mostly occurred in sarcomere proteins and nuclear-localized proteins associated with contractile dysfunction and cardiac hypertrophy. Seven aberrant phosphosites were observed at the z-disk binding region of titin. Additional agarose gel analysis showed that while total titin cardiac expression remained unaltered, its stiffer N2B isoform was significantly increased in HFpEF vs. Sham (0.144 ± 0.01 vs. 0.127 ± 0.01; P < 0.05). In summary, this study demonstrates marked changes in proteins related to mitochondrial metabolism and the cardiac contractile apparatus in HFpEF. We propose that SIRT3 may play a role in perpetuating these changes and may be a target for drug development in HFpEF.
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Affiliation(s)
- María Valero-Muñoz
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
- *Correspondence: María Valero-Muñoz,
| | - Eng Leng Saw
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
| | - Ryan M. Hekman
- Department of Biology, Boston University, Boston, MA, United States
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
| | - Benjamin C. Blum
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
- Center for Network Systems Biology, Boston University, Boston, MA, United States
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Andrew Emili
- Department of Biology, Boston University, Boston, MA, United States
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
| | - Flora Sam
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
- Flora Sam,
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3
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Guo J, Wu J, Wei D, Wang T, Hu Y, Lin Y, Chen M, Yang L, Wen Y, Cai Y, Xu X, Li H, Wu S, Xie X. Association between greenness and dyslipidemia in patients with coronary heart disease: A proteomic approach. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113199. [PMID: 35042090 DOI: 10.1016/j.ecoenv.2022.113199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Residential surrounding greenness may be protective of dyslipidemia are often theorized but remain poorly quantified. In particular, the underlying biological mechanisms of blood lipid changes with green spaces remain unclear. METHODS Our observational epidemiology study included a residentially stable sample of 1035 coronary heart disease patients, and proteomics study included 16 participants. Normalized Difference Vegetation Index (NDVI) was used to evaluate residential greenness exposures. Proteomics technology was used to identify plasma greenness-related proteome disturbance, and the pathway analysis was employed to evaluate the potential biological mechanisms of greenness decreasing dyslipidemia risk. RESULT Higher residential surrounding greenness in the 500-m area was associated with lower risks of dyslipidemia (odds ratio (OR) = 0.871, 95% confidence interval (CI): 0.763, 0.994 for per one-quartile NDVI increase). Lymphocytes mediated 18.7% of the association between greenness and dyslipidemia. Greenness related proteins (including PLXDC1, IGFBP2 and LY6D) may regulate the biological functions of lipid metabolism and transport-related proteins (including ADIPOQ and CES1) through a series of biological processes. CONCLUSION People in greener surroundings have a lower risk of dyslipidemia, which may be due to their lower inflammation, stronger lipid transporter activity, and normal cholesterol metabolism.
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Affiliation(s)
- Jianhui Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jieyu Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Donghong Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Tinggui Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yuduan Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yawen Lin
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Mingjun Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Le Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yeyin Wen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yingying Cai
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Xingyan Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Huanyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Siying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Xiaoxu Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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4
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de Brevern AG, Rebehmed J. Current status of PTMs structural databases: applications, limitations and prospects. Amino Acids 2022; 54:575-590. [PMID: 35020020 DOI: 10.1007/s00726-021-03119-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
Abstract
Protein 3D structures, determined by their amino acid sequences, are the support of major crucial biological functions. Post-translational modifications (PTMs) play an essential role in regulating these functions by altering the physicochemical properties of proteins. By virtue of their importance, several PTM databases have been developed and released in decades, but very few of these databases incorporate real 3D structural data. Since PTMs influence the function of the protein and their aberrant states are frequently implicated in human diseases, providing structural insights to understand the influence and dynamics of PTMs is crucial for unraveling the underlying processes. This review is dedicated to the current status of databases providing 3D structural data on PTM sites in proteins. Some of these databases are general, covering multiple types of PTMs in different organisms, while others are specific to one particular type of PTM, class of proteins or organism. The importance of these databases is illustrated with two major types of in silico applications: predicting PTM sites in proteins using machine learning approaches and investigating protein structure-function relationships involving PTMs. Finally, these databases suffer from multiple problems and care must be taken when analyzing the PTMs data.
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Affiliation(s)
- Alexandre G de Brevern
- Université de Paris, INSERM, UMR_S 1134, DSIMB, 75739, Paris, France.,Université de la Réunion, INSERM, UMR_S 1134, DSIMB, 97715, Saint-Denis de La Réunion, France.,Laboratoire d'Excellence GR-Ex, 75739, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
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5
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Zhang H, Viveiros A, Nikhanj A, Nguyen Q, Wang K, Wang W, Freed DH, Mullen JC, MacArthur R, Kim DH, Tymchak W, Sergi CM, Kassiri Z, Wang S, Oudit GY. The Human Explanted Heart Program: A translational bridge for cardiovascular medicine. Biochim Biophys Acta Mol Basis Dis 2021; 1867:165995. [PMID: 33141063 PMCID: PMC7581399 DOI: 10.1016/j.bbadis.2020.165995] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
The progression of cardiovascular research is often impeded by the lack of reliable disease models that fully recapitulate the pathogenesis in humans. These limitations apply to both in vitro models such as cell-based cultures and in vivo animal models which invariably are limited to simulate the complexity of cardiovascular disease in humans. Implementing human heart tissue in cardiovascular research complements our research strategy using preclinical models. We established the Human Explanted Heart Program (HELP) which integrates clinical, tissue and molecular phenotyping thereby providing a comprehensive evaluation into human heart disease. Our collection and storage of biospecimens allow them to retain key pathogenic findings while providing novel insights into human heart failure. The use of human non-failing control explanted hearts provides a valuable comparison group for the diseased explanted hearts. Using HELP we have been able to create a tissue repository which have been used for genetic, molecular, cellular, and histological studies. This review describes the process of collection and use of explanted human heart specimens encompassing a spectrum of pediatric and adult heart diseases, while highlighting the role of these invaluable specimens in translational research. Furthermore, we highlight the efficient procurement and bio-preservation approaches ensuring analytical quality of heart specimens acquired in the context of heart donation and transplantation.
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Affiliation(s)
- Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Anissa Viveiros
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Anish Nikhanj
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Quynh Nguyen
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Kaiming Wang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Wei Wang
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Darren H Freed
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - John C Mullen
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Roderick MacArthur
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel H Kim
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Wayne Tymchak
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Consolato M Sergi
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Anatomical Pathology, Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Zamaneh Kassiri
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Shaohua Wang
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada.
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6
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Wang X, Shen X, Weil BR, Young RF, Canty JM, Qu J. Quantitative proteomic and phosphoproteomic profiling of ischemic myocardial stunning in swine. Am J Physiol Heart Circ Physiol 2020; 318:H1256-H1271. [PMID: 32223553 DOI: 10.1152/ajpheart.00713.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite decades of research on the pathophysiology of myocardial stunning, protein changes and/or phosphorylation status underlying alterations in cardiac function/structure remain inadequately understood. Here, we utilized comprehensive and quantitative proteomic and phosphoproteomic approaches to explore molecular mechanisms of myocardial stunning in swine. The closed-chest swine (n = 5 pigs) were subjected to a 10-min left anterior descending coronary artery (LAD) occlusion producing regional myocardial stunning. Tissues from the ischemic LAD region and a remote nonischemic area of the left ventricle were collected 1 h after reperfusion. Ion current-based proteomics (IonStar) and quantitative phosphoproteomics were employed in parallel to identify alterations in protein level and site-specific phosphorylation changes. A novel swine heart protein database exhibiting high accuracy and low redundancy was developed here to facilitate comprehensive study. Further informatic investigations identified potential protein-protein interactions in stunned myocardium. In total, we quantified 2,099 protein groups and 4,699 phosphorylation sites with only 0.4% missing values. Proteomic analyses revealed downregulation of contractile function and extracellular matrix remodeling. Meanwhile, alterations in phosphorylation linked with contractile dysfunction and apoptotic cell death were uncovered. NetworKIN/STRING analysis predicted regulatory kinases responsible for altered phosphosites, such as protein kinase C-mediated phosphorylation of cardiac troponin I-S199 and CaMKII-mediated phosphorylation of phospholamban-T17. In summary, the ion current-based proteomics and phosphoproteomics reliably identified novel alterations in protein content and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium, which corroborate well with our physiological observations. Moreover, this work developed a comprehensive database of the swine heart proteome, a highly valuable resource for future translational research in porcine models with cardiovascular diseases.NEW & NOTEWORTHY We first used ion current-based proteomics and phosphoproteomics to reliably identify novel alterations in protein expression and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium and developed a comprehensive swine heart-specific proteome database, which provides a valuable resource for future research in porcine models of cardiovascular diseases.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York
| | - Xiaomeng Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Brian R Weil
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York
| | - Rebeccah F Young
- Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - John M Canty
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System, Buffalo, New York.,Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jun Qu
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York.,Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York
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7
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Lim SH, Lee J, Han MJ. Comprehensive analysis of the cardiac proteome in a rat model of myocardial ischemia-reperfusion using a TMT-based quantitative proteomic strategy. Proteome Sci 2020; 18:2. [PMID: 32165865 PMCID: PMC7060589 DOI: 10.1186/s12953-020-00158-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/26/2020] [Indexed: 12/29/2022] Open
Abstract
Background Traditional studies of the cardiac proteome have mainly investigated in an animal model by two-dimensional gel electrophoresis (2-DE). However, the results have not been of satisfactory quality for an understanding of the underlying mechanism. Recent quantitative proteomic methods have been improved to overcome these limitations. To comprehensively study the cardiac proteome in a rat model of ischemia-reperfusion (IR), we developed a tandem mass tag (TMT)-based quantitative proteomic strategy. Furthermore, using this strategy, we examined the molecular mechanisms underlying the prevention of myocardial infarction by the intake of Triticum aestivum L. extract (TALE), a representative dietary fiber grain. Methods Cardiac proteomes were analyzed by 2-DE as a gel-based approach, and TMT labeling coupled with two-dimensional liquid chromatography (2D-LC) and tandem mass spectrometry (MS/MS) as a non-gel-based quantitative approach. Additionally, gene ontology annotation was conducted by PANTHER database. Several proteins of interest were verified by a Western blot analysis. Results Total 641 proteins were identified commonly from two independent MS datasets using 2D-LC MS/MS. Among these, we identified 151 IR-related proteins that were differentially expressed between the sham-operation group and IR group, comprising 62 up-regulated proteins and 89 down-regulated proteins. Most of the reduced proteins were involved in metabolic processes. In addition, 57 of the IR-related proteins were affected by TALE intake, representing 25 up-regulated proteins and 32 down-regulated proteins. In particular, TALE intake leads to a switch in metabolism to reduce the loss of high-energy phosphates and the accumulation of harmful catabolites (especially reactive oxygen species (ROS)) and to maintain cytoskeleton balance, leading to a reduction in cardiac IR injury. Conclusions Our study provides a comprehensive proteome map of IR-related proteins and potential target proteins and identifies mechanisms implicated in the prevention of myocardial infarction by TALE intake in a rat IR model.
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Affiliation(s)
- Sun Ha Lim
- 1Department of Biochemistry, School of Medicine, Catholic University of Daegu, 33, 17-gil, Duryugongwon-ro, Nam-gu, Daegu, 42472 Republic of Korea
| | - Jongwon Lee
- 1Department of Biochemistry, School of Medicine, Catholic University of Daegu, 33, 17-gil, Duryugongwon-ro, Nam-gu, Daegu, 42472 Republic of Korea
| | - Mee-Jung Han
- 2Department of Biomolecular and Chemical Engineering, Dongyang University, 145 Dongyang-daero, Punggi-eup, Yeongju, Gyeongbuk 36040 Republic of Korea.,3Department of Nursing, Dongyang University, 145 Dongyang-daero, Punggi-eup, Yeongju, Gyeongbuk 36040 Republic of Korea
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8
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Daniels LJ, Varma U, Annandale M, Chan E, Mellor KM, Delbridge LMD. Myocardial Energy Stress, Autophagy Induction, and Cardiomyocyte Functional Responses. Antioxid Redox Signal 2019; 31:472-486. [PMID: 30417655 DOI: 10.1089/ars.2018.7650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Energy stress in the myocardium occurs in a variety of acute and chronic pathophysiological contexts, including ischemia, nutrient deprivation, and diabetic disease settings of substrate disturbance. Although the heart is highly adaptive and flexible in relation to fuel utilization and routes of adenosine-5'-triphosphate (ATP) generation, maladaptations in energy stress situations confer functional deficit. An understanding of the mechanisms that link energy stress to impaired myocardial performance is crucial. Recent Advances: Emerging evidence suggests that, in parallel with regulated enzymatic pathways that control intracellular substrate supply, other processes of "bulk" autophagic macromolecular breakdown may be important in energy stress conditions. Recent findings indicate that cargo-specific autophagic activity may be important in different stress states. In particular, induction of glycophagy, a glycogen-specific autophagy, has been described in acute and chronic energy stress situations. The impact of elevated cardiomyocyte glucose flux relating to glycophagy dysregulation on contractile function is unknown. Critical Issues: Ischemia- and diabetes-related cardiac adverse events comprise the majority of cardiovascular disease morbidity and mortality. Current therapies involve management of systemic comorbidities. Cardiac-specific adjunct treatments targeted to manage myocardial energy stress responses are lacking. Future Directions: New knowledge is required to understand the mechanisms involved in selective recruitment of autophagic responses in the cardiomyocyte energy stress response. In particular, exploration of the links between cell substrate flux, calcium ion (Ca2+) flux, and phagosomal cargo flux is required. Strategies to target specific fuel "bulk" management defects in cardiac energy stress states may be of therapeutic value.
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Affiliation(s)
- Lorna J Daniels
- 1 Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Upasna Varma
- 2 Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Marco Annandale
- 1 Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Eleia Chan
- 2 Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Kimberley M Mellor
- 1 Department of Physiology, University of Auckland, Auckland, New Zealand.,2 Department of Physiology, University of Melbourne, Melbourne, Australia.,3 Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Lea M D Delbridge
- 2 Department of Physiology, University of Melbourne, Melbourne, Australia
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9
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Schmidt W, Cammarato A. The actin 'A-triad's' role in contractile regulation in health and disease. J Physiol 2019; 598:2897-2908. [PMID: 30770548 DOI: 10.1113/jp276741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
Striated muscle contraction is regulated by Ca2+ -dependent modulation of myosin cross-bridge binding to F-actin by the thin filament troponin (Tn)-tropomyosin (Tm) complex. In the absence of Ca2+ , Tn binds to actin and constrains Tm to an azimuthal location where it sterically occludes myosin binding sites along the thin filament surface. This limits force production and promotes muscle relaxation. In addition to Tn-actin interactions, inhibitory Tm positioning requires associations between other thin filament constituents. For example, the actin 'A-triad', composed of residues K326, K328 and R147, forms numerous, highly favourable electrostatic contacts with Tm that are critical for establishing its inhibitory azimuthal binding position. Here, we review recent findings, including the identification and interrogation of modifications within and proximal to the A-triad that are associated with disease and/or altered muscle behaviour, which highlight the surface feature's role in F-actin-Tm interactions and contractile regulation.
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Affiliation(s)
- William Schmidt
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, 21205, Baltimore, MD, USA
| | - Anthony Cammarato
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, 21205, Baltimore, MD, USA.,Department of Physiology, Johns Hopkins University School of Medicine, 733 N Broadway, 21205, Baltimore, MD, USA
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10
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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11
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12
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Abstract
PURPOSE OF REVIEW Cardiac troponin (cTn) plays an essential role for assessment of outcome in acute coronary syndrome (ACS). However, the prognostic value of cTn is not absolute. In this mini-review, we summarize the evidence on the utility of established biomarkers of left-ventricular dysfunction, hemodynamic stress, inflammation, and renal dysfunction for risk prediction beyond cTn in ACS. RECENT FINDINGS Only few biomarkers consistently demonstrate additive prognostic value to cTn levels. The B-type natriuretic peptides (NPs) and growth-differentiation factor-15 (GDF-15) are most promising in this regard. However, there are uncertainties regarding the role of these biomarkers for guidance of treatment decisions, and their prognostic increment to cTn levels measured with high-sensitivity assays is largely unknown. The NPs and GDF-15 provide the strongest prognostic increment to cTn levels in ACS. However, the role of these biomarkers for clinical decision-making in contemporary settings has still to be defined.
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Affiliation(s)
- K M Eggers
- Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, S-751 85, Uppsala, Sweden.
| | - B Lindahl
- Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, S-751 85, Uppsala, Sweden
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13
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Cheow ESH, Cheng WC, Yap T, Dutta B, Lee CN, Kleijn DPVD, Sorokin V, Sze SK. Myocardial Injury Is Distinguished from Stable Angina by a Set of Candidate Plasma Biomarkers Identified Using iTRAQ/MRM-Based Approach. J Proteome Res 2017; 17:499-515. [DOI: 10.1021/acs.jproteome.7b00651] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Esther Sok Hwee Cheow
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Woo Chin Cheng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
| | - Terence Yap
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Bamaprasad Dutta
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Chuen Neng Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Cardiac, Thoracic & Vascular Surgery, National University Heart Centre, Singapore 119074, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Dominique P. V. de Kleijn
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Vascular Surgery, University Medical Center Utrecht, The Netherlands & Interuniversity Cardiovascular Institute of The Netherlands, Utrecht 3508 GA, The Netherlands
| | - Vitaly Sorokin
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Cardiac, Thoracic & Vascular Surgery, National University Heart Centre, Singapore 119074, Singapore
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
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14
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Mokou M, Lygirou V, Vlahou A, Mischak H. Proteomics in cardiovascular disease: recent progress and clinical implication and implementation. Expert Rev Proteomics 2017; 14:117-136. [DOI: 10.1080/14789450.2017.1274653] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marika Mokou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Harald Mischak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Mosaiques Diagnostics, Hannover, Germany
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15
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Lam MPY, Lau E, Ng DCM, Wang D, Ping P. Cardiovascular proteomics in the era of big data: experimental and computational advances. Clin Proteomics 2016; 13:23. [PMID: 27980500 PMCID: PMC5137214 DOI: 10.1186/s12014-016-9124-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/24/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond merely inventorying protein species, and address sophisticated questions on cardiac physiology. The advent of massive mass spectrometry datasets has in turn led to increasing intersection between proteomics and big data science. Here we review new frontiers in technological developments and their applications to cardiovascular medicine. The impact of big data science on cardiovascular proteomics investigations and translation to medicine is highlighted.
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Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Edward Lau
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Dominic C M Ng
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Ding Wang
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Peipei Ping
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Medicine, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Bioinformatics, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
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16
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Abstract
The last decade has seen a surge in publications describing novel biomarkers for early detection of diabetic nephropathy (DN), but as yet none have outperformed albuminuria in well-designed prospective studies. This is partially attributable to our incomplete understanding of the many complex interrelated mechanisms underlying DN development, a heterogeneous process unlikely to be captured by a single biomarker. Proteomics offers the advantage of simultaneously analysing the entire protein content of a biological sample, and the technique has gained attention as a potential tool for a more accurate diagnosis of disease at an earlier stage as well as a means by which to unravel the pathogenesis of complex diseases such as DN using an untargeted approach. This review will discuss the potential of proteomics as both a clinical and research tool, evaluating exploratory work in animal models as well as diagnostic potential in human subjects.
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Affiliation(s)
- G Currie
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK.
| | - C Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
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17
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Grammatikakis I, Abdelmohsen K, Gorospe M. Posttranslational control of HuR function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27307117 DOI: 10.1002/wrna.1372] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022]
Abstract
The RNA-binding protein HuR (human antigen R) associates with numerous transcripts, coding and noncoding, and controls their splicing, localization, stability, and translation. Through its regulation of target transcripts, HuR has been implicated in cellular events including proliferation, senescence, differentiation, apoptosis, and the stress and immune responses. In turn, HuR influences processes such as cancer and inflammation. HuR function is primarily regulated through posttranslational modifications that alter its subcellular localization and its ability to bind target RNAs; such modifications include phosphorylation, methylation, ubiquitination, NEDDylation, and proteolytic cleavage. In this review, we describe the modifications that impact upon HuR function on gene expression programs and disease states. WIREs RNA 2017, 8:e1372. doi: 10.1002/wrna.1372 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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18
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Nagai-Okatani C, Minamino N. Aberrant Glycosylation in the Left Ventricle and Plasma of Rats with Cardiac Hypertrophy and Heart Failure. PLoS One 2016; 11:e0150210. [PMID: 27281159 PMCID: PMC4900630 DOI: 10.1371/journal.pone.0150210] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/20/2016] [Indexed: 11/21/2022] Open
Abstract
Targeted proteomics focusing on post-translational modifications, including glycosylation, is a useful strategy for discovering novel biomarkers. To apply this strategy effectively to cardiac hypertrophy and resultant heart failure, we aimed to characterize glycosylation profiles in the left ventricle and plasma of rats with cardiac hypertrophy. Dahl salt-sensitive hypertensive rats, a model of hypertension-induced cardiac hypertrophy, were fed a high-salt (8% NaCl) diet starting at 6 weeks. As a result, they exhibited cardiac hypertrophy at 12 weeks and partially impaired cardiac function at 16 weeks compared with control rats fed a low-salt (0.3% NaCl) diet. Gene expression analysis revealed significant changes in the expression of genes encoding glycosyltransferases and glycosidases. Glycoproteome profiling using lectin microarrays indicated upregulation of mucin-type O-glycosylation, especially disialyl-T, and downregulation of core fucosylation on N-glycans, detected by specific interactions with Amaranthus caudatus and Aspergillus oryzae lectins, respectively. Upregulation of plasma α-l-fucosidase activity was identified as a biomarker candidate for cardiac hypertrophy, which is expected to support the existing marker, atrial natriuretic peptide and its related peptides. Proteomic analysis identified cysteine and glycine-rich protein 3, a master regulator of cardiac muscle function, as an O-glycosylated protein with altered glycosylation in the rats with cardiac hypertrophy, suggesting that alternations in O-glycosylation affect its oligomerization and function. In conclusion, our data provide evidence of significant changes in glycosylation pattern, specifically mucin-type O-glycosylation and core defucosylation, in the pathogenesis of cardiac hypertrophy and heart failure, suggesting that they are potential biomarkers for these diseases.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
| | - Naoto Minamino
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka, Japan
- * E-mail:
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19
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Manakov D, Ujcikova H, Pravenec M, Novotny J. Alterations in the cardiac proteome of the spontaneously hypertensive rat induced by transgenic expression of CD36. J Proteomics 2016; 145:177-186. [PMID: 27132684 DOI: 10.1016/j.jprot.2016.04.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 01/08/2023]
Abstract
Fatty acid translocase (FAT/CD36) plays an important role in fatty acid uptake by different cell types and may also participate in regulation of calcium homeostasis and eicosanoid production. CD36 deficiency or polymorphisms in the CD36 gene are linked to some physiological irregularities. It is known that the expression of FAT/CD36 is aberrant in the spontaneously hypertensive rat (SHR), one of the most widely studied rat strains in cardiovascular research. In this work, we compared the cardiac proteome of SHR and transgenic SHR-Cd36 rats, who carry a copy of the wild type CD36 gene. Protein expression profiling was based on two-dimensional gel electrophoresis (2DE) coupled to tandem mass spectrometry and label-free LC/MS. These two complementary proteomic approaches allowed us to investigate proteome differences in the left and right heart ventricles of SHR and SHR-Cd36 rats. In total, we identified 26 differently expressed myocardial proteins, out of which 18 were found in the right ventricles and 8 in the left ventricles. Besides that, we determined a great number of proteins uniquely expressed either in the left or right ventricles. These data indicate a large qualitative disparity between the left and right ventricles. Genetic manipulations may affect different proteins in both heart ventricles. Biological significance: This is the first report revealing a relatively broad impact of transgenic expression of CD36 on the heart at the proteome level. Comparison of the protein profiles in both the left and right ventricles revealed differences in several proteins involved especially in energy metabolism. The observed downregulation of the respiratory chain enzymes in transgenic SHR-Cd36 rats may suggest a shift in regulation of energy metabolism due to expression of fatty acid translocase FAT/CD36. This study highlights the important role of cardiac tissue proteomic profiling for mapping of proteins which might be altered by targeted genetic manipulations.
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Affiliation(s)
- Dmitry Manakov
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic
| | - Hana Ujcikova
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic; Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University in Prague, Czech Republic.
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20
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Abstract
Advances in mass spectrometry technology and bioinformatics using clinical human samples have expanded quantitative proteomics in cardiovascular research. There are two major proteomic strategies: namely, "gel-based" or "gel-free" proteomics coupled with either "top-down" or "bottom-up" mass spectrometry. Both are introduced into the proteomic analysis using plasma or serum sample targeting 'biomarker" searches of aortic aneurysm and tissue samples, such as from the aneurysmal wall, calcific aortic valve, or myocardial tissue, investigating pathophysiological protein interactions and post-translational modifications. We summarize the proteomic studies that analyzed human samples taken during cardiovascular surgery to investigate disease processes, in order to better understand the system-wide changes behind known molecular factors and specific signaling pathways.
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Affiliation(s)
- Teiji Oda
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Ken-ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Izumo, Shimane, Japan
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21
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Kim EH, Galchev VI, Kim JY, Misek SA, Stevenson TK, Campbell MD, Pagani FD, Day SM, Johnson TC, Washburn JG, Vikstrom KL, Michele DE, Misek DE, Westfall MV. Differential protein expression and basal lamina remodeling in human heart failure. Proteomics Clin Appl 2016; 10:585-96. [PMID: 26756417 DOI: 10.1002/prca.201500099] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing protein expression in ischemic failing (F) and nonfailing (NF) human hearts. EXPERIMENTAL DESIGN Protein expression differences were investigated using multidimensional protein identification and validated by Western analysis. This approach detected basal lamina (BL) remodeling, and further studies analyzed samples for evidence of structural BL remodeling. A rat model of pressure overload (PO) was studied to determine whether nonischemic stressors also produce BL remodeling and impact cellular adhesion. RESULTS Differential protein expression of collagen IV, laminin α2, and nidogen-1 indicated BL remodeling develops in F versus NF hearts Periodic disruption of cardiac myocyte BL accompanied this process in F, but not NF heart. The rat PO myocardium also developed BL remodeling and compromised myocyte adhesion compared to sham controls. CONCLUSIONS AND CLINICAL RELEVANCE Differential protein expression and evidence of structural and functional BL alterations develop during heart failure. The compromised adhesion associated with this remodeling indicates a high potential for dysfunctional cellular integrity and tethering in failing myocytes. Therapeutically targeting BL remodeling could slow or prevent the progression of heart disease.
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Affiliation(s)
- Evelyn H Kim
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Sean A Misek
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Tamara K Stevenson
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Matthew D Campbell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Francis D Pagani
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Sharlene M Day
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - T Craig Johnson
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Joseph G Washburn
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Vikstrom
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.,Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David E Misek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
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22
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Lindoso RS, Sandim V, Collino F, Carvalho AB, Dias J, da Costa MR, Zingali RB, Vieyra A. Proteomics of cell-cell interactions in health and disease. Proteomics 2015; 16:328-44. [PMID: 26552723 DOI: 10.1002/pmic.201500341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
The mechanisms of cell-cell communications are now under intense study by proteomic approaches. Proteomics has unraveled changes in protein profiling as the result of cell interactions mediated by ligand/receptor, hormones, soluble factors, and the content of extracellular vesicles. Besides being a brief overview of the main and profitable methodologies now available (evaluating theory behind the methods, their usefulness, and pitfalls), this review focuses on-from a proteome perspective-some signaling pathways and post-translational modifications (PTMs), which are essential for understanding ischemic lesions and their recovery in two vital organs in mammals, the heart, and the kidney. Knowledge of misdirection of the proteome during tissue recovery, such as represented by the convergence between fibrosis and cancer, emerges as an important tool in prognosis. Proteomics of cell-cell interaction is also especially useful for understanding how stem cells interact in injured tissues, anticipating clues for rational therapeutic interventions. In the effervescent field of induced pluripotency and cell reprogramming, proteomic studies have shown what proteins from specialized cells contribute to the recovery of infarcted tissues. Overall, we conclude that proteomics is at the forefront in helping us to understand the mechanisms that underpin prevalent pathological processes.
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Affiliation(s)
- Rafael S Lindoso
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Vanessa Sandim
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Federica Collino
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, Turin, Italy.,Translational Center of Regenerative Medicine, University of Turin/Fresenius Medical Care, Turin, Italy
| | - Adriana B Carvalho
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Juliana Dias
- National Institute of Cancer, Rio de Janeiro, RJ, Brazil
| | - Milene R da Costa
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Russolina B Zingali
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Proteomic Network of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Translational Biomedicine Graduate Program, Grand Rio University, Duque de Caxias, RJ, Brazil
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23
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Identification and validation of argininosuccinate synthase as a candidate urinary biomarker for major depressive disorder. Clin Chim Acta 2015; 451:142-8. [DOI: 10.1016/j.cca.2015.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/17/2015] [Accepted: 09/17/2015] [Indexed: 12/22/2022]
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24
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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25
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An integrated metabonomic and proteomic study on Kidney-Yin Deficiency Syndrome patients with diabetes mellitus in China. Acta Pharmacol Sin 2015; 36:689-98. [PMID: 25937635 DOI: 10.1038/aps.2014.169] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/08/2014] [Indexed: 11/08/2022] Open
Abstract
AIM To investigate specific changes in metabolites and proteins of Kidney-Yin Deficiency Syndrome (KYDS) patients with diabetes mellitus (DM) in China. METHODS KYDS (n=29) and non-KYDS (n=23) patients with DM were recruited for this study. The KYDS was diagnosed by two senior TCM clinicians separately. The metabonomic and proteomic profiles of the patients were assessed using a metabonomic strategy based on NMR with multivariate analysis and a proteomic strategy based on MALDI-TOF-MS, respectively. RESULTS Eighteen upregulated peptides and thirty downregulated peptides were observed in the plasma of the KYDS patients. Comparing the proteomic profiles of the KYDS and non-KYDS groups, however, no significantly differentially expressed peptides were found. At the same time, major metabolic alterations were found to distinguish the two groups, including eight significantly changed metabolites (creatinine, citrate, TMAO, phenylalanine, tyrosine, alanine, glycine and taurine). The levels of creatinine, citrate, TMAO, phenylalanine and tyrosine were decreased, whereas the levels of alanine, glycine and taurine were increased in the KYDS patients. These biochemical changes were found to be associated with alterations in amino acid metabolism, energy metabolism and gut microflora. CONCLUSION The identification of distinct expression profiles of metabolites and signaling pathways in KYDS patients with DM suggests that there are indeed molecular signatures underlying the principles of 'Syndrome Differentiation' in traditional Chinese medicine.
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26
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Schoenhoff F, Carrel T. How are you feeling today? Quality of life after aortic surgery. Eur J Cardiothorac Surg 2015; 49:389-90. [PMID: 25920463 DOI: 10.1093/ejcts/ezv174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Florian Schoenhoff
- Department of Cardiovascular Surgery, University Hospital Bern, Bern, Switzerland
| | - Thierry Carrel
- Department of Cardiovascular Surgery, University Hospital Bern, Bern, Switzerland
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27
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Viswanathan MC, Blice-Baum AC, Schmidt W, Foster DB, Cammarato A. Pseudo-acetylation of K326 and K328 of actin disrupts Drosophila melanogaster indirect flight muscle structure and performance. Front Physiol 2015; 6:116. [PMID: 25972811 PMCID: PMC4412121 DOI: 10.3389/fphys.2015.00116] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/26/2015] [Indexed: 01/13/2023] Open
Abstract
In striated muscle tropomyosin (Tm) extends along the length of F-actin-containing thin filaments. Its location governs access of myosin binding sites on actin and, hence, force production. Intermolecular electrostatic associations are believed to mediate critical interactions between the proteins. For example, actin residues K326, K328, and R147 were predicted to establish contacts with E181 of Tm. Moreover, K328 also potentially forms direct interactions with E286 of myosin when the motor is strongly bound. Recently, LC-MS/MS analysis of the cardiac acetyl-lysine proteome revealed K326 and K328 of actin were acetylated, a post-translational modification (PTM) that masks the residues' inherent positive charges. Here, we tested the hypothesis that by removing the vital actin charges at residues 326 and 328, the PTM would perturb Tm positioning and/or strong myosin binding as manifested by altered skeletal muscle function and structure in the Drosophila melanogaster model system. Transgenic flies were created that permit tissue-specific expression of K326Q, K328Q, or K326Q/K328Q acetyl-mimetic actin and of wild-type actin via the UAS-GAL4 bipartite expression system. Compared to wild-type actin, muscle-restricted expression of mutant actin had a dose-dependent effect on flight ability. Moreover, excessive K328Q and K326Q/K328Q actin overexpression induced indirect flight muscle degeneration, a phenotype consistent with hypercontraction observed in other Drosophila myofibrillar mutants. Based on F-actin-Tm and F-actin-Tm-myosin models and on our physiological data, we conclude that acetylating K326 and K328 of actin alters electrostatic associations with Tm and/or myosin and thereby augments contractile properties. Our findings highlight the utility of Drosophila as a model that permits efficient targeted design and assessment of molecular and tissue-specific responses to muscle protein modifications, in vivo.
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Affiliation(s)
- Meera C Viswanathan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Anna C Blice-Baum
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - William Schmidt
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - D Brian Foster
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Anthony Cammarato
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine Baltimore, MD, USA
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28
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Xu Y, Yao B, Shi K, Lu J, Jin Y, Qi B, Li H, Pan S, Chen L, Ma C. Phosphorylation of Serine422 increases the stability and transactivation activities of human Osterix. FEBS Lett 2015; 589:857-64. [PMID: 25728276 DOI: 10.1016/j.febslet.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 11/19/2022]
Abstract
Osterix (Osx) is an essential regulator for osteoblast differentiation and bone formation. Although phosphorylation has been reported to be involved in the regulation of Osx activity, the precise underlying mechanisms remain to be elucidated. Here we identified S422 as a novel phosphorylation site of Osx and demonstrated that GSK-3β interacted and co-localized with Osx. GSK-3β increased the stability and transactivation activity of Osx through phosphorylation of the newly identified site. These findings expanded our understanding of the mechanisms of posttranslational regulation of Osx and the role of GSK-3β in the control of Osx transactivation activity.
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Affiliation(s)
- Yuexin Xu
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Bing Yao
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Kaikai Shi
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Jianlei Lu
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Yucui Jin
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Bing Qi
- Department of Oral Pathology, Affiliated Hospital of Stomatology, Nanjing Medical University, Hanzhong Road 136, Nanjing 210029, P.R. China
| | - Hongwei Li
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Hanzhong Road 136, Nanjing 210029, P.R. China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P.R. China
| | - Li Chen
- Molecular Endocrinology Laboratory, Department of Endocrinology, Odense University Hospital, Winslowparken 25. Sal 1, DK-5000 Odense C, Denmark
| | - Changyan Ma
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China.
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Schneck NA, Lowenthal M, Phinney K, Lee SB. Current trends in magnetic particle enrichment for mass spectrometry-based analysis of cardiovascular protein biomarkers. Nanomedicine (Lond) 2015; 10:433-46. [DOI: 10.2217/nnm.14.188] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Magnetic particles have traditionally been utilized to isolate and enrich various cardiovascular protein biomarkers for mass spectrometry-based proteomic analysis. The application of functionalized magnetic particles for immunocapture is attractive due to their easy manipulation, large surface area-to-volume ratios for maximal antibody binding, good recovery and high magnetic saturation. Magnetic particle enrichment coupled with mass spectrometry can act as a complementary tool for clinical sandwich-immunoassay development since it can provide improved target specificity and true metrological traceability. The purpose of this review is to summarize current separation methods and technologies that use magnetic particles to enrich protein biomarkers from complex matrices, specifically focusing on cardiovascular disease-related proteins and the advantages of magnetic particles over existing techniques.
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Affiliation(s)
- Nicole A Schneck
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Mark Lowenthal
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Karen Phinney
- Biomolecular Measurement Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA
| | - Sang Bok Lee
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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Moreno-Gonzalo O, Villarroya-Beltri C, Sánchez-Madrid F. Post-translational modifications of exosomal proteins. Front Immunol 2014; 5:383. [PMID: 25157254 PMCID: PMC4128227 DOI: 10.3389/fimmu.2014.00383] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/28/2014] [Indexed: 11/26/2022] Open
Abstract
Exosomes mediate intercellular communication and participate in many cell processes such as cancer progression, immune activation or evasion, and the spread of infection. Exosomes are small vesicles secreted to the extracellular environment through the release of intraluminal vesicles contained in multivesicular bodies (MVBs) upon the fusion of these MVBs with the plasma membrane. The composition of exosomes is not random, suggesting that the incorporation of cargo into them is a regulated process. However, the mechanisms that control the sorting of protein cargo into exosomes are currently elusive. Here, we review the post-translational modifications detected in exosomal proteins, and discuss their possible role in their specific sorting into exosomes.
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Affiliation(s)
- Olga Moreno-Gonzalo
- Vascular Biology and Inflammation Department, Centro Nacional de Investigaciones Cardiovasculares , Madrid , Spain ; Servicio de Inmunología, Hospital de la Princesa, Instituto de Investigación Sanitaria de la Princesa, Universidad Autónoma de Madrid , Madrid , Spain
| | - Carolina Villarroya-Beltri
- Vascular Biology and Inflammation Department, Centro Nacional de Investigaciones Cardiovasculares , Madrid , Spain ; Servicio de Inmunología, Hospital de la Princesa, Instituto de Investigación Sanitaria de la Princesa, Universidad Autónoma de Madrid , Madrid , Spain
| | - Francisco Sánchez-Madrid
- Vascular Biology and Inflammation Department, Centro Nacional de Investigaciones Cardiovasculares , Madrid , Spain ; Servicio de Inmunología, Hospital de la Princesa, Instituto de Investigación Sanitaria de la Princesa, Universidad Autónoma de Madrid , Madrid , Spain
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Shen X, Young R, Canty JM, Qu J. Quantitative proteomics in cardiovascular research: global and targeted strategies. Proteomics Clin Appl 2014; 8:488-505. [PMID: 24920501 DOI: 10.1002/prca.201400014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/02/2014] [Accepted: 06/06/2014] [Indexed: 11/05/2022]
Abstract
Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here, we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation.
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Affiliation(s)
- Xiaomeng Shen
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
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Qu J, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models. J Proteome Res 2014; 13:2571-84. [PMID: 24697261 PMCID: PMC4015685 DOI: 10.1021/pr5000472] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Hibernating
myocardium is an adaptive response to repetitive myocardial
ischemia that is clinically common, but the mechanism of adaptation
is poorly understood. Here we compared the proteomes of hibernating
versus normal myocardium in a porcine model with 24 biological replicates.
Using the ion-current-based proteomic strategy optimized in this study
to expand upon previous proteomic work, we identified differentially
expressed proteins in new molecular pathways of cardiovascular interest.
The methodological strategy includes efficient extraction with detergent
cocktail; precipitation/digestion procedure with high, quantitative
peptide recovery; reproducible nano-LC/MS analysis on a long, heated
column packed with small particles; and quantification based on ion-current
peak areas. Under the optimized conditions, high efficiency and reproducibility
were achieved for each step, which enabled a reliable comparison of
24 the myocardial samples. To achieve confident discovery of differentially
regulated proteins in hibernating myocardium, we used highly stringent
criteria to define “quantifiable proteins”. These included
the filtering criteria of low peptide FDR and S/N > 10 for peptide
ion currents, and each protein was quantified independently from ≥2
distinct peptides. For a broad methodological validation, the quantitative
results were compared with a parallel, well-validated 2D-DIGE analysis
of the same model. Excellent agreement between the two orthogonal
methods was observed (R = 0.74), and the ion-current-based
method quantified almost one order of magnitude more proteins. In
hibernating myocardium, 225 significantly altered proteins were discovered
with a low false-discovery rate (∼3%). These proteins are involved
in biological processes including metabolism, apoptosis, stress response,
contraction, cytoskeleton, transcription, and translation. This provides
compelling evidence that hibernating myocardium adapts to chronic
ischemia. The major metabolic mechanisms include a down-regulation
of mitochondrial respiration and an increase in glycolysis. Meanwhile,
cardioprotective and cytoskeletal proteins are increased, while cardiomyocyte
contractile proteins are reduced. These intrinsic adaptations to regional
ischemia maintain long-term cardiomyocyte viability at the expense
of contractile function.
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Affiliation(s)
- Jun Qu
- Department of Pharmaceutical Sciences, ‡Department of Biochemistry, §Department of Medicine, ∥Department of Physiology and Biophysics, ⊥The Center for Research in Cardiovascular Medicine, and #Center for Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo , Buffalo, New York 14214, United States
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Abstract
The most common markers for monitoring patients with diabetes are glucose and HbA1c, but additional markers such as glycated human serum albumin (HSA) have been identified that could address the glycation gap and bridge the time scales of glycemia between transient and 2-3 months. However, there is currently no technical platform that could measure these markers concurrently in a cost-effective manner. We have developed a new assay that is able to measure glucose, HbA1c, glycated HSA, and glycated apolipoprotein A-I (apoA-I) for monitoring of individual blood glycemia, as well as cysteinylated HSA, S-nitrosylated HbA, and methionine-oxidized apoA-I for gauging oxidative stress and cardiovascular risks, all in 5 μL of blood. The assay utilizes our proprietary multinozzle emitter array chip technology to enable the analysis of small volumes of blood, without complex sample preparation prior to the online and on-chip liquid chromatography-nanoelectrospray ionization mass spectrometry. Importantly, the assay employs top-down proteomics for more accurate quantitation of protein levels and for identification of post-translational modifications. Further, the assay provides multimarker, multitime-scale, and multicompartment monitoring of blood glycemia. Our assay readily segregates healthy controls from Type 2 diabetes patients and may have the potential to enable better long-term monitoring and disease management of diabetes.
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Affiliation(s)
- Pan Mao
- Newomics Inc. , 5980 Horton Street, Suite 525, Emeryville, California 94608, United States
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35
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Quantitative profiling of the rat heart myoblast secretome reveals differential responses to hypoxia and re-oxygenation stress. J Proteomics 2014; 98:138-49. [DOI: 10.1016/j.jprot.2013.12.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 11/18/2022]
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Wijeratne AB, Manning JR, Schultz JEJ, Greis KD. Quantitative phosphoproteomics using acetone-based peptide labeling: method evaluation and application to a cardiac ischemia/reperfusion model. J Proteome Res 2013; 12:4268-79. [PMID: 24016359 DOI: 10.1021/pr400835k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mass spectrometry (MS) techniques to globally profile protein phosphorylation in cellular systems that are relevant to physiological or pathological changes have been of significant interest in biological research. An MS-based strategy utilizing an inexpensive acetone-based peptide-labeling technique known as reductive alkylation by acetone (RABA) for quantitative phosphoproteomics was explored to evaluate its capacity. Because the chemistry for RABA labeling for phosphorylation profiling had not been previously reported, it was first validated using a standard phosphoprotein and identical phosphoproteomes from cardiac tissue extracts. A workflow was then utilized to compare cardiac tissue phosphoproteomes from mouse hearts not expressing FGF2 versus hearts expressing low-molecular-weight fibroblast growth factor-2 (LMW FGF2) to relate low-molecular-weight fibroblast growth factor-2 (LMW FGF2)-mediated cardioprotective phenomena induced by ischemia/reperfusion injury of hearts, with downstream phosphorylation changes in LMW FGF2 signaling cascades. Statistically significant phosphorylation changes were identified at 14 different sites on 10 distinct proteins, including some with mechanisms already established for LMW FGF2-mediated cardioprotective signaling (e.g., connexin-43), some with new details linking LMW FGF2 to the cardioprotective mechanisms (e.g., cardiac myosin binding protein C or cMyBPC), and also several new downstream effectors not previously recognized for cardio-protective signaling by LMW FGF2. Additionally, one of the phosphopeptides, cMyBPC/pSer-282, identified was further verified with site-specific quantification using an SRM (selected reaction monitoring)-based approach that also relies on isotope labeling of a synthetic phosphopeptide with deuterated acetone as an internal standard. Overall, this study confirms that the inexpensive acetone-based peptide labeling can be used in both exploratory and targeted quantification phosphoproteomic studies to identify and verify biologically relevant phosphorylation changes in whole tissues.
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Affiliation(s)
- Aruna B Wijeratne
- Department of Cancer Biology and ‡Department of Pharmacology & Cell Biophysics, University of Cincinnati College of Medicine , 3125 Eden Avenue,Cincinnati, Ohio 45267, United States
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Barallobre-Barreiro J, Chung YL, Mayr M. La proteómica y la metabolómica: los mecanismos de la enfermedad cardiovascular y el descubrimiento de biomarcadores. Rev Esp Cardiol 2013. [DOI: 10.1016/j.recesp.2013.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Barallobre-Barreiro J, Chung YL, Mayr M. Proteomics and metabolomics for mechanistic insights and biomarker discovery in cardiovascular disease. REVISTA ESPANOLA DE CARDIOLOGIA (ENGLISH ED.) 2013; 66:657-61. [PMID: 24776335 DOI: 10.1016/j.rec.2013.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 04/18/2013] [Indexed: 01/24/2023]
Abstract
In the last decade, proteomics and metabolomics have contributed substantially to our understanding of cardiovascular diseases. The unbiased assessment of pathophysiological processes without a priori assumptions complements other molecular biology techniques that are currently used in a reductionist approach. In this review, we highlight some of the "omics" methods used to assess protein and metabolite changes in cardiovascular disease. A discrete biological function is very rarely attributed to a single molecule; more often it is the combined input of many proteins. In contrast to the reductionist approach, in which molecules are studied individually, "omics" platforms allow the study of more complex interactions in biological systems. Combining proteomics and metabolomics to quantify changes in metabolites and their corresponding enzymes will advance our understanding of pathophysiological mechanisms and aid the identification of novel biomarkers for cardiovascular disease.
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Affiliation(s)
| | - Yuen-Li Chung
- Cancer Research UK and EPSRC Cancer Imaging Centre, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College of London, London, United Kingdom.
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Chang YW, Chang YT, Wang Q, Lin JJC, Chen YJ, Chen CC. Quantitative phosphoproteomic study of pressure-overloaded mouse heart reveals dynamin-related protein 1 as a modulator of cardiac hypertrophy. Mol Cell Proteomics 2013; 12:3094-107. [PMID: 23882026 DOI: 10.1074/mcp.m113.027649] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Pressure-overload stress to the heart causes pathological cardiac hypertrophy, which increases the risk of cardiac morbidity and mortality. However, the detailed signaling pathways induced by pressure overload remain unclear. Here we used phosphoproteomics to delineate signaling pathways in the myocardium responding to acute pressure overload and chronic hypertrophy in mice. Myocardial samples at 4 time points (10, 30, 60 min and 2 weeks) after transverse aortic banding (TAB) in mice underwent quantitative phosphoproteomics assay. Temporal phosphoproteomics profiles showed 360 phosphorylation sites with significant regulation after TAB. Multiple mechanical stress sensors were activated after acute pressure overload. Gene ontology analysis revealed differential phosphorylation between hearts with acute pressure overload and chronic hypertrophy. Most interestingly, analysis of the cardiac hypertrophy pathway revealed phosphorylation of the mitochondrial fission protein dynamin-related protein 1 (DRP1) by prohypertrophic kinases. Phosphorylation of DRP1 S622 was confirmed in TAB-treated mouse hearts and phenylephrine (PE)-treated rat neonatal cardiomyocytes. TAB-treated mouse hearts showed phosphorylation-mediated mitochondrial translocation of DRP1. Inhibition of DRP1 with the small-molecule inhibitor mdivi-1 reduced the TAB-induced hypertrophic responses. Mdivi-1 also prevented PE-induced hypertrophic growth and oxygen consumption in rat neonatal cardiomyocytes. We reveal the signaling responses of the heart to pressure stress in vivo and in vitro. DRP1 may be important in the development of cardiac hypertrophy.
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Affiliation(s)
- Yu-Wang Chang
- Molecular Medicine Program, Taiwan International Graduate Program, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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40
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Bleijerveld OB, Zhang YN, Beldar S, Hoefer IE, Sze SK, Pasterkamp G, de Kleijn DPV. Proteomics of plaques and novel sources of potential biomarkers for atherosclerosis. Proteomics Clin Appl 2013; 7:490-503. [DOI: 10.1002/prca.201200119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/07/2013] [Accepted: 03/30/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Onno B. Bleijerveld
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ya-Nan Zhang
- Surgery & Cardiovascular Research Institute; National University (NUS) & National University Hospital (NUH); Singapore
| | - Serap Beldar
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Imo E. Hoefer
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Siu K. Sze
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
| | - Dominique P. V. de Kleijn
- Laboratory of Experimental Cardiology; University Medical Center Utrecht; Utrecht the Netherlands
- Surgery & Cardiovascular Research Institute; National University (NUS) & National University Hospital (NUH); Singapore
- Interuniversity Cardiology Institute of the Netherlands; Utrecht the Netherlands
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41
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Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF. Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics 2013; 86:97-104. [PMID: 23684787 DOI: 10.1016/j.jprot.2013.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 11/17/2022]
Abstract
UNLABELLED Trypanosomatid parasites of the genus Leishmania cause severe human diseases collectively termed leishmaniasis. Parasite ATP-binding proteins have emerged as potent targets for chemotherapeutic intervention. However, many parasite-specific ATP-binding proteins may escape current efforts in drug target identification, validation and deconvolution due to the lack of sequence conservation and functional annotation of these proteins in early branching eukaryotic trypanosomatids. Here, we selectively enriched for ATP-binding proteins from Leishmania donovani axenic promastigote and amastigote total protein extracts utilizing a Capture Compound™ (CC) linked to the ATP-competitive inhibitor staurosporine. As judged by in-gel kinase activity assay and competitive inhibition with free staurosporine, the CC specifically enriched for parasite phosphotransferases. Comparative nanoLC-MS(n) analysis identified 70 captured proteins, including 24 conserved protein kinases, and 32 hypothetical proteins with potential ATP-binding function. We identified conserved signature sequence motifs characteristic for staurosporine-binding protein kinases, and identified the hypothetical proteins LinJ.20.0280 and LinJ.09.1630 as novel ATP-binding proteins. Thus, functional enrichment procedures such as described here, combined with bio-informatics analyses and activity assays, provide powerful tools for the discovery of parasite-specific ATP-binding proteins that escape homology-based identification, which can be subsequently targeted for pharmacological intervention. BIOLOGICAL SIGNIFICANCE Functional enrichment using a Capture Compound™ linked to the ATP-competitive inhibitor staurosporine provides a powerful new tool for the discovery of parasite-specific ATP-binding proteins that escape homology-based identification, which can be subsequently targeted for pharmacological intervention.
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Affiliation(s)
- Olivier Leclercq
- Institut Pasteur, and CNRS URA2581, Department of Parasitology and Mycology, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
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42
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Napoli C, Zullo A, Picascia A, Infante T, Mancini FP. Recent advances in proteomic technologies applied to cardiovascular disease. J Cell Biochem 2013; 114:7-20. [PMID: 22886784 DOI: 10.1002/jcb.24307] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022]
Abstract
In recent years, the diagnosis of cardiovascular disease (CVD) has increased its potential, also thanks to mass spectrometry (MS) proteomics. Modern MS proteomics tools permit analyzing a variety of biological samples, ranging from single cells to tissues and body fluids, like plasma and urine. This approach enhances the search for informative biomarkers in biological samples from apparently healthy individuals or patients, thus allowing an earlier and more precise diagnosis and a deeper comprehension of pathogenesis, development and outcome of CVD to further reduce the enormous burden of this disease on public health. In fact, many differences in protein expression between CVD-affected and healthy subjects have been detected, but only a few of them have been useful to establish clinical biomarkers because they did not pass the verification and validation tests. For a concrete clinical support of MS proteomics to CVD, it is, therefore, necessary to: ameliorate the resolution, sensitivity, specificity, throughput, precision, and accuracy of MS platform components; standardize procedures for sample collection, preparation, and analysis; lower the costs of the analyses; reduce the time of biomarker verification and validation. At the same time, it will be fundamental, for the future perspectives of proteomics in clinical trials, to define the normal protein maps and the global patterns of normal protein levels, as well as those specific for the different expressions of CVD.
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Affiliation(s)
- Claudio Napoli
- Department of General Pathology, Excellence Research Centre on Cardiovascular Disease, U.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology [SIMT], Regional Reference Laboratory of Transplant Immunology [LIT], Azienda Ospedaliera Universitaria (AOU), 1st School of Medicine, Second University of Naples, 80138 Naples, Italy.
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43
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44
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Huang G, Zhou Y, Zhang Y, Li BQ, Zhang N, Cai YD. Prediction of carbamylated lysine sites based on the one-class k-nearest neighbor method. MOLECULAR BIOSYSTEMS 2013; 9:2729-40. [DOI: 10.1039/c3mb70195f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
The following represent a selection of the most read
Circulation Research
articles published between January 2010 and December 2011, presented in reverse order of publication. Articles were selected based on the number of Full Text/PDF downloads, adjusted to compensate for differences in the length of time articles have been available online.
As stated in the past, our motivation in compiling such lists of most read articles is multifarious. By highlighting these articles, we wish to direct the attention of our readers to new information that may be of particular interest to a large fraction of the community of cardiovascular scholars. In addition, a synopsis of the most popular articles can be a useful indicator of burgeoning areas of research that are likely to dominate the landscape for years to come. This “honor roll” is also meant to acknowledge the outstanding work of the authors and their efforts in advancing the frontiers of cardiovascular science. Furthermore, we believe that the articles highlighted below represent paradigms of scientific excellence, particularly with respect to the three criteria that we value most at
Circulation Research
: conceptual and/or mechanistic novelty, scientific impact, and methodological rigor. Finally, we hope that this list will provide tangible evidence of the high (and rising) level of scientific excellence of the work published in
Circulation Research
.
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Comparative proteomic analysis of plasma from major depressive patients: identification of proteins associated with lipid metabolism and immunoregulation. Int J Neuropsychopharmacol 2012; 15:1413-25. [PMID: 22717272 DOI: 10.1017/s1461145712000302] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Major depressive disorder is a common neuropsychiatric disorder contributing to several socio-economic burdens including disability and suicide. As the underlying pathophysiology of major depressive disorder remains unclear, no objective test is yet available for aiding diagnosis or monitoring disease progression. To contribute to a better understanding of its pathogenesis, a comparative proteomic study was performed to identify proteins differentially expressed in plasma samples obtained from first-onset, treatment-naive depressed patients as compared to healthy controls. Samples from the two groups were immunodepleted of seven high-abundance proteins, labelled with isobaric tags for relative and absolute quantitation and then analysed by multi-dimensional liquid chromatography-tandem mass spectrometry. The proteomic results were further validated by immunoblotting or enzyme-linked immunoadsorbent assays and analysed with the MetaCore database. The results demonstrate that the functions of the altered proteins are primarily involved in lipid metabolism and immunoregulation. These findings suggest that early perturbation of lipid metabolism and immunoregulation may be involved in the pathophysiology of major depressive disorder.
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Chugh S, Sharma P, Kislinger T, Gramolini AO. Clinical proteomics: getting to the heart of the matter. ACTA ACUST UNITED AC 2012; 5:377. [PMID: 22715282 DOI: 10.1161/circgenetics.110.957761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Shaan Chugh
- Department of Physiology, University of Toronto, ON, Canada
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Affiliation(s)
- Ayesha I. De Souza
- From the Cardiovascular Sciences Research Centre, St. George’s University of London, London, United Kingdom
| | - A. John Camm
- From the Cardiovascular Sciences Research Centre, St. George’s University of London, London, United Kingdom
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49
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Xin F, Radivojac P. Post-translational modifications induce significant yet not extreme changes to protein structure. ACTA ACUST UNITED AC 2012; 28:2905-13. [PMID: 22947645 DOI: 10.1093/bioinformatics/bts541] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION A number of studies of individual proteins have shown that post-translational modifications (PTMs) are associated with structural rearrangements of their target proteins. Although such studies provide critical insights into the mechanics behind the dynamic regulation of protein function, they usually feature examples with relatively large conformational changes. However, with the steady growth of Protein Data Bank (PDB) and available PTM sites, it is now possible to more systematically characterize the role of PTMs as conformational switches. In this study, we ask (1) what is the expected extent of structural change upon PTM, (2) how often are those changes in fact substantial, (3) whether the structural impact is spatially localized or global and (4) whether different PTMs have different signatures. RESULTS We exploit redundancy in PDB and, using root-mean-square deviation, study the conformational heterogeneity of groups of protein structures corresponding to identical sequences in their unmodified and modified forms. We primarily focus on the two most abundant PTMs in PDB, glycosylation and phosphorylation, but show that acetylation and methylation have similar tendencies. Our results provide evidence that PTMs induce conformational changes at both local and global level. However, the proportion of large changes is unexpectedly small; only 7% of glycosylated and 13% of phosphorylated proteins undergo global changes >2 Å. Further analysis suggests that phosphorylation stabilizes protein structure by reducing global conformational heterogeneity by 25%. Overall, these results suggest a subtle but common role of allostery in the mechanisms through which PTMs affect regulatory and signaling pathways. CONTACT predrag@indiana.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fuxiao Xin
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
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Helsens K, Martens L. Enabling computational proteomics by public and local data management systems. ACTA ACUST UNITED AC 2012; 5:266. [PMID: 22511708 DOI: 10.1161/circgenetics.110.957837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kenny Helsens
- Department of Medical Protein Research, VIB, and Department of Biochemistry, Ghent University, Ghent, Belgium
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