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Basak T, Varshney S, Akhtar S, Sengupta S. Understanding different facets of cardiovascular diseases based on model systems to human studies: a proteomic and metabolomic perspective. J Proteomics 2015; 127:50-60. [PMID: 25956427 DOI: 10.1016/j.jprot.2015.04.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/08/2015] [Accepted: 04/25/2015] [Indexed: 02/02/2023]
Abstract
UNLABELLED Cardiovascular disease has remained as the largest cause of morbidity and mortality worldwide. From dissecting the disease aetiology to identifying prognostic markers for better management of the disease is still a challenge for researchers. In the post human genome sequencing era much of the thrust has been focussed towards application of advanced genomic tools along with evaluation of traditional risk factors. With the advancement of next generation proteomics and metabolomics approaches it has now become possible to understand the protein interaction network & metabolic rewiring which lead to the perturbations of the disease phenotype. Further, elucidating different post translational modifications using advanced mass spectrometry based methods have provided an impetus towards in depth understanding of the proteome. The past decade has observed a plethora of studies where proteomics has been applied successfully to identify potential prognostic and diagnostic markers as well as to understand the disease mechanisms for various types of cardiovascular diseases. In this review, we attempted to document relevant proteomics based studies that have been undertaken either to identify potential biomarkers or have elucidated newer mechanistic insights into understanding the patho-physiology of cardiovascular disease, primarily coronary artery disease, cardiomyopathy, and myocardial ischemia. We have also provided a perspective on the potential of proteomics in combating this deadly disease. BIOLOGICAL SIGNIFICANCE This review has catalogued recent studies on proteomics and metabolomics involved in understanding several cardiovascular diseases (CVDs). A holistic systems biology based approach, of which proteomics and metabolomics are two very important components, would help in delineating various pathways associated with complex disorders like CVD. This would ultimately provide better mechanistic understanding of the disease biology leading to development of prognostic biomarkers. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India.
| | - Swati Varshney
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India
| | - Shamima Akhtar
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India.
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102
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Valeja SG, Xiu L, Gregorich ZR, Guner H, Jin S, Ge Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem 2015; 87:5363-5371. [PMID: 25867201 PMCID: PMC4575680 DOI: 10.1021/acs.analchem.5b00657] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To address the complexity of the proteome in mass spectrometry (MS)-based top-down proteomics, multidimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the complexity of the proteome. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IEC-HIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 nonredundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore, this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics.
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Affiliation(s)
- Santosh G. Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
| | - Huseyin Guner
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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103
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Costa ADF, Franco OL. Insights into RNA transcriptome profiling of cardiac tissue in obesity and hypertension conditions. J Cell Physiol 2015; 230:959-68. [PMID: 25393239 DOI: 10.1002/jcp.24807] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/05/2014] [Indexed: 12/20/2022]
Abstract
Several epidemiologic studies suggest that obesity and hypertension are associated with cardiac transcriptome modifications that could be further associated with inflammatory processes and cardiac hypertrophy. In this field, transcriptome studies have demonstrated their importance to elucidate physiologic mechanisms, pathways or genes involved in many biologic processes. Over the past decade, RNA microarray and RNA-seq analysis has become an essential component to examine metabolic pathways in terms of mRNA expression in cardiology. In this review, cardiac muscle gene expression in response to effects of obesity and hypertension will be focused, providing a broad view on cardiac transcriptome and physiologic and biochemical mechanisms involved in gene expression changes produced by these events, emphasizing the use of new technologies for gene expression analyses.
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Affiliation(s)
- Alzenira de Fátima Costa
- Universidade Católica de Brasília, Pós-Graduação em Ciências Genômicas e Biotecnologia Centro de Análises Proteômicas e Bioquímicas, Brasília, Brazil
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104
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Arentz G, Weiland F, Oehler MK, Hoffmann P. State of the art of 2D DIGE. Proteomics Clin Appl 2015; 9:277-88. [DOI: 10.1002/prca.201400119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/13/2014] [Accepted: 11/10/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Georgia Arentz
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Florian Weiland
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Martin K. Oehler
- School of Paediatrics and Reproductive Health; Research Centre for Reproductive Health; Robinson Institute; University of Adelaide; SA Australia
- Department of Gynaecological Oncology; Royal Adelaide Hospital; Adelaide SA Australia
| | - Peter Hoffmann
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
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105
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Hwang L, Ayaz-Guner S, Gregorich ZR, Cai W, Valeja SG, Jin S, Ge Y. Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles. J Am Chem Soc 2015; 137:2432-5. [PMID: 25655481 DOI: 10.1021/ja511833y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Analysis of protein phosphorylation remains a significant challenge due to the low abundance of phosphoproteins and the low stoichiometry of phosphorylation, which requires effective enrichment of phosphoproteins. Here we have developed superparamagnetic nanoparticles (NPs) whose surface is functionalized by multivalent ligand molecules that specifically bind to the phosphate groups on any phosphoproteins. These NPs enrich phosphoproteins from complex cell and tissue lysates with high specificity as confirmed by SDS-PAGE analysis with a phosphoprotein-specific stain and mass spectrometry analysis of the enriched phosphoproteins. This method enables universal and effective capture, enrichment, and detection of intact phosphoproteins toward a comprehensive analysis of the phosphoproteome.
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Affiliation(s)
- Leekyoung Hwang
- Department of Chemistry, ‡Department of Cell and Regenerative Biology, §Molecular and Cellular Pharmacology Program, and ∥Human Proteomics Program, University of Wisconsin-Madison , Madison, Wisconsin 53719, United States
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106
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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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107
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Chang YH, Gregorich ZR, Chen AJ, Hwang L, Guner H, Yu D, Zhang J, Ge Y. New mass-spectrometry-compatible degradable surfactant for tissue proteomics. J Proteome Res 2015; 14:1587-99. [PMID: 25589168 DOI: 10.1021/pr5012679] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue proteomics is increasingly recognized for its role in biomarker discovery and disease mechanism investigation. However, protein solubility remains a significant challenge in mass spectrometry (MS)-based tissue proteomics. Conventional surfactants such as sodium dodecyl sulfate (SDS), the preferred surfactant for protein solubilization, are not compatible with MS. Herein, we have screened a library of surfactant-like compounds and discovered an MS-compatible degradable surfactant (MaSDeS) for tissue proteomics that solubilizes all categories of proteins with performance comparable to SDS. The use of MaSDeS in the tissue extraction significantly improves the total number of protein identifications from commonly used tissues, including tissue from the heart, liver, and lung. Notably, MaSDeS significantly enriches membrane proteins, which are often under-represented in proteomics studies. The acid degradable nature of MaSDeS makes it amenable for high-throughput MS-based proteomics. In addition, the thermostability of MaSDeS allows for its use in experiments requiring high temperature to facilitate protein extraction and solubilization. Furthermore, we have shown that MaSDeS outperforms the other MS-compatible surfactants in terms of overall protein solubility and the total number of identified proteins in tissue proteomics. Thus, the use of MaSDeS will greatly advance tissue proteomics and realize its potential in basic biomedical and clinical research. MaSDeS could be utilized in a variety of proteomics studies as well as general biochemical and biological experiments that employ surfactants for protein solubilization.
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Affiliation(s)
- Ying-Hua Chang
- Department of Cell and Regenerative Biology, ‡Molecular and Cellular Pharmacology Program, §Department of Chemistry, ∥Human Proteomics Program, and ⊥Molecular and Environmental Toxicology Program, University of Wisconsin-Madison , 1300 University Avenue, Madison 53706, Wisconsin, United States
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108
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Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J Muscle Res Cell Motil 2015; 36:169-81. [PMID: 25613324 DOI: 10.1007/s10974-015-9404-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/07/2015] [Indexed: 01/26/2023]
Abstract
Skeletal muscles are the most abundant tissues in the human body. They are composed of a heterogeneous collection of muscle fibers that perform various functions. Skeletal muscle troponin (sTn) regulates skeletal muscle contraction and relaxation. sTn consists of 3 subunits, troponin I (TnI), troponin T (TnT), and troponin C (TnC). TnI inhibits the actomyosin Mg(2+)-ATPase, TnC binds Ca(2+), and TnT is the tropomyosin (Tm)-binding subunit. The cardiac and skeletal isoforms of Tn share many similarities but the roles of modifications of Tn in the two muscles may differ. The modifications of cardiac Tn are known to alter muscle contractility and have been well-characterized. However, the modification status of sTn remains unclear. Here, we have employed top-down mass spectrometry (MS) to decipher the modifications of human sTnT and sTnI. We have extensively characterized sTnT and sTnI proteoforms, including alternatively spliced isoforms and post-translationally modified forms, found in human skeletal muscle with high mass accuracy and comprehensive sequence coverage. Moreover, we have localized the phosphorylation site of slow sTnT isoform III to Ser1 by tandem MS with electron capture dissociation. This is the first study to comprehensively characterize human sTn and also the first to identify the basal phosphorylation site for human sTnT by top-down MS.
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109
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Zhang J, Reza Malmirchegini G, Clubb RTCT, Loo JA. Native top-down mass spectrometry for the structural characterization of human hemoglobin. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:221-31. [PMID: 26307702 PMCID: PMC4731028 DOI: 10.1255/ejms.1340] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and noncovalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down MS using electrospray ionization and a 15-Tesla Fourier transform ion cyclotron resonance mass spectrometer. Native MS preserves the noncovalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of the Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore a low fragmentation efficiency. Precursor ion activation allows a steady increase in N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and four z ions on the α chain; 36 c ions and two z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer shows similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. It may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.
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Affiliation(s)
| | | | - Robert T Clubb T Clubb
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, 90095, United States.
| | - Joseph A Loo
- De partment of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine, UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, 90095, United States.
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110
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Gregorich ZR, Ge Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics 2014; 14:1195-210. [PMID: 24723472 DOI: 10.1002/pmic.201300432] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/10/2014] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of PTMs and sequence variations, make such analyses challenging. An emerging "top-down" MS-based proteomics approach, which provides a "bird's eye" view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for the unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as underdeveloped data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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111
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Stienen GJM. Pathomechanisms in heart failure: the contractile connection. J Muscle Res Cell Motil 2014; 36:47-60. [PMID: 25376563 DOI: 10.1007/s10974-014-9395-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/20/2014] [Indexed: 01/07/2023]
Abstract
Heart failure is a multi-factorial progressive disease in which eventually the contractile performance of the heart is insufficient to meet the demands of the body, even at rest. A distinction can be made on the basis of the cause of the disease in genetic and acquired heart failure and at the functional level between systolic and diastolic heart failure. Here the basic determinants of contractile function of myocardial cells will be reviewed and an attempt will be made to elucidate their role in the development of heart failure. The following topics are addressed: the tension generating capacity, passive tension, the rate of tension development, the rate of ATP utilisation, calcium sensitivity of tension development, phosphorylation of contractile proteins, length dependent activation and stretch activation. The reduction in contractile performance during systole can be attributed predominantly to a loss of cardiomyocytes (necrosis), myocyte disarray and a decrease in myofibrillar density all resulting in a reduction in the tension generating capacity and likely also to a mismatch between energy supply and demand of the myocardium. This leads to a decline in the ejection fraction of the heart. Diastolic dysfunction can be attributed to fibrosis and an increase in titin stiffness which result in an increase in stiffness of the ventricular wall and hampers the filling of the heart with blood during diastole. A large number of post translation modifications of regulatory sarcomeric proteins influence myocardial function by altering calcium sensitivity of tension development. It is still unclear whether in concert these influences are adaptive or maladaptive during the disease process.
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Affiliation(s)
- G J M Stienen
- Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands,
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112
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Mahr C, Gundry RL. Hold or fold--proteins in advanced heart failure and myocardial recovery. Proteomics Clin Appl 2014; 9:121-33. [PMID: 25331159 DOI: 10.1002/prca.201400100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/17/2014] [Accepted: 10/14/2014] [Indexed: 12/14/2022]
Abstract
Advanced heart failure (AHF) describes the subset of heart failure patients refractory to conventional medical therapy. For some AHF patients, the use of mechanical circulatory support (MCS) provides an intermediary "bridge" step for transplant-eligible patients or an alternative therapy for transplant-ineligible patients. Over the past 20 years, clinical observations have revealed that approximately 1% of patients with MCS undergo significant reverse remodeling to the point where the device can be explanted. Unfortunately, it is unclear why some patients experience durable, sustained myocardial remission, while others redevelop heart failure (i.e. which hearts "hold" and which hearts "fold"). In this review, we outline unmet clinical needs related to treating patients with MCS, provide an overview of protein dynamics in the reverse-remodeling process, and propose specific areas where we expect MS and proteomic analyses will have significant impact on our understanding of disease progression, molecular mechanisms of recovery, and provide new markers with prognostic value that can positively impact patient care. Complimentary perspectives are provided with the goal of making this important topic accessible and relevant to both a clinical and basic science audience, as the intersection of these disciplines is required to advance the field.
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Affiliation(s)
- Claudius Mahr
- Division of Cardiology, University of Washington, Seattle, WA, USA
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113
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Wijnker PJM, Murphy AM, Stienen GJM, van der Velden J. Troponin I phosphorylation in human myocardium in health and disease. Neth Heart J 2014; 22:463-9. [PMID: 25200323 PMCID: PMC4188840 DOI: 10.1007/s12471-014-0590-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Cardiac troponin I (cTnI) is well known as a biomarker for the diagnosis of myocardial damage. However, because of its central role in the regulation of contraction and relaxation in heart muscle, cTnI may also be a potential target for the treatment of heart failure. Studies in rodent models of cardiac disease and human heart samples showed altered phosphorylation at various sites on cTnI (i.e. site-specific phosphorylation). This is caused by altered expression and/or activity of kinases and phosphatases during heart failure development. It is not known whether these (transient) alterations in cTnI phosphorylation are beneficial or detrimental. Knowledge of the effects of site-specific cTnI phosphorylation on cardiomyocyte contractility is therefore of utmost importance for the development of new therapeutic strategies in patients with heart failure. In this review we focus on the role of cTnI phosphorylation in the healthy heart upon activation of the beta-adrenergic receptor pathway (as occurs during increased stress and exercise) and as a modulator of the Frank-Starling mechanism. Moreover, we provide an overview of recent studies which aimed to reveal the functional consequences of changes in cTnI phosphorylation in cardiac disease.
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Affiliation(s)
- P J M Wijnker
- Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Van der Boechorststraat 7, 1081, BT, Amsterdam, the Netherlands,
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114
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The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C. Proc Natl Acad Sci U S A 2014; 111:14412-7. [PMID: 25246568 DOI: 10.1073/pnas.1410775111] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cardiac isoform of troponin I (cTnI) has a unique 31-residue N-terminal region that binds cardiac troponin C (cTnC) to increase the calcium sensitivity of the sarcomere. The interaction can be abolished by cTnI phosphorylation at Ser22 and Ser23, an important mechanism for regulating cardiac contractility. cTnC contains two EF-hand domains (the N and C domain of cTnC, cNTnC and cCTnC) connected by a flexible linker. Calcium binding to either domain favors an "open" conformation, exposing a large hydrophobic surface that is stabilized by target binding, cTnI[148-158] for cNTnC and cTnI[39-60] for cCTnC. We used multinuclear multidimensional solution NMR spectroscopy to study cTnI[1-73] in complex with cTnC. cTnI[39-60] binds to the hydrophobic face of cCTnC, stabilizing an alpha helix in cTnI[41-67] and a type VIII turn in cTnI[38-41]. In contrast, cTnI[1-37] remains disordered, although cTnI[19-37] is electrostatically tethered to the negatively charged surface of cNTnC (opposite its hydrophobic surface). The interaction does not directly affect the calcium binding affinity of cNTnC. However, it does fix the positioning of cNTnC relative to the rest of the troponin complex, similar to what was previously observed in an X-ray structure [Takeda S, et al. (2003) Nature 424(6944):35-41]. Domain positioning impacts the effective concentration of cTnI[148-158] presented to cNTnC, and this is how cTnI[19-37] indirectly modulates the calcium affinity of cNTnC within the context of the cardiac thin filament. Phosphorylation of cTnI at Ser22/23 disrupts domain positioning, explaining how it impacts many other cardiac regulatory mechanisms, like the Frank-Starling law of the heart.
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115
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Ramirez-Correa GA, Martinez-Ferrando MI, Zhang P, Murphy AM. Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications. Proteomics Clin Appl 2014; 8:543-53. [DOI: 10.1002/prca.201400034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/29/2014] [Accepted: 06/24/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Genaro A. Ramirez-Correa
- Department of Pediatrics/Division of Cardiology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | | | - Pingbo Zhang
- The Hopkins Bayview Proteomics Center; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Anne M. Murphy
- Department of Pediatrics/Division of Cardiology; Johns Hopkins University School of Medicine; Baltimore MD USA
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116
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Xiu L, Valeja SG, Alpert A, Jin S, Ge Y. Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal Chem 2014; 86:7899-906. [PMID: 24968279 PMCID: PMC4144745 DOI: 10.1021/ac501836k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/26/2014] [Indexed: 01/16/2023]
Abstract
One of the challenges in proteomics is the proteome's complexity, which necessitates the fractionation of proteins prior to the mass spectrometry (MS) analysis. Despite recent advances in top-down proteomics, separation of intact proteins remains challenging. Hydrophobic interaction chromatography (HIC) appears to be a promising method that provides high-resolution separation of intact proteins, but unfortunately the salts conventionally used for HIC are incompatible with MS. In this study, we have identified ammonium tartrate as a MS-compatible salt for HIC with comparable separation performance as the conventionally used ammonium sulfate. Furthermore, we found that the selectivity obtained with ammonium tartrate in the HIC mobile phases is orthogonal to that of reverse phase chromatography (RPC). By coupling HIC and RPC as a novel two-dimensional chromatographic method, we have achieved effective high-resolution intact protein separation as demonstrated with standard protein mixtures and a complex cell lysate. Subsequently, the separated intact proteins were identified by high-resolution top-down MS. For the first time, these results have shown the high potential of HIC as a high-resolution protein separation method for top-down proteomics.
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Affiliation(s)
- Lichen Xiu
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Santosh G. Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Andrew
J. Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- PolyLC Inc., Columbia 21045, Maryland, United States
| | - Song Jin
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Ying Ge
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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117
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Valkevich E, Sanchez NA, Ge Y, Strieter ER. Middle-down mass spectrometry enables characterization of branched ubiquitin chains. Biochemistry 2014; 53:4979-89. [PMID: 25023374 PMCID: PMC4372068 DOI: 10.1021/bi5006305] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/09/2014] [Indexed: 12/22/2022]
Abstract
Protein ubiquitylation, one of the most prevalent post-translational modifications in eukaryotes, is involved in regulating nearly every cellular signaling pathway. The vast functional range of ubiquitylation has largely been attributed to the formation of a diverse array of polymeric ubiquitin (polyUb) chains. Methods that enable the characterization of these diverse chains are necessary to fully understand how differences in structure relate to function. Here, we describe a method for the detection of enzymatically derived branched polyUb conjugates in which a single Ub subunit is modified by two Ub molecules at distinct lysine residues. Using a middle-down mass spectrometry approach in which restricted trypsin-mediated digestion is coupled with mass spectrometric analysis, we characterize the polyUb chains produced by bacterial effector E3 ligases NleL (non-Lee-encoded effector ligase from enterohemorrhagic Escherichia coli O157:H7) and IpaH9.8 (from Shigella flexneri). Because Ub is largely intact after minimal trypsinolysis, multiple modifications on a single Ub moiety can be detected. Analysis of NleL- and IpaH9.8-derived polyUb chains reveals branch points are present in approximately 10% of the overall chain population. When unanchored, well-defined polyUb chains are added to reaction mixtures containing NleL, longer chains are more likely to be modified internally, forming branch points rather than extending from the end of the chain. These results suggest that middle-down mass spectrometry can be used to assess the extent to which branched polyUb chains are formed by various enzymatic systems and potentially evaluate the presence of these atypical conjugates in cell and tissue extracts.
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Affiliation(s)
- Ellen
M. Valkevich
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas A. Sanchez
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department
of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin—Madison, 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Eric R. Strieter
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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118
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Ying P, Serife AG, Deyang Y, Ying G. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Proteomics Clin Appl 2014; 8:554-68. [PMID: 24945106 PMCID: PMC4231170 DOI: 10.1002/prca.201400043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
Myofilaments are composed of thin and thick filaments that coordinate with each other to regulate muscle contraction and relaxation. PTMs together with genetic variations and alternative splicing of the myofilament proteins play essential roles in regulating cardiac contractility in health and disease. Therefore, a comprehensive characterization of the myofilament proteins in physiological and pathological conditions is essential for better understanding the molecular basis of cardiac function and dysfunction. Due to the vast complexity and dynamic nature of proteins, it is challenging to obtain a holistic view of myofilament protein modifications. In recent years, top-down MS has emerged as a powerful approach to study isoform composition and PTMs of proteins owing to its advantage of complete sequence coverage and its ability to identify PTMs and sequence variants without a priori knowledge. In this review, we will discuss the application of top-down MS to the study of cardiac myofilaments and highlight the insights it provides into the understanding of molecular mechanisms in contractile dysfunction of heart failure. Particularly, recent results of cardiac troponin and tropomyosin modifications will be elaborated. The limitations and perspectives on the use of top-down MS for myofilament protein characterization will also be briefly discussed.
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Affiliation(s)
- Peng Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ayaz-Guner Serife
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Yu Deyang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ge Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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119
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Wijnker PJM, Sequeira V, Witjas-Paalberends ER, Foster DB, dos Remedios CG, Murphy AM, Stienen GJM, van der Velden J. Phosphorylation of protein kinase C sites Ser42/44 decreases Ca(2+)-sensitivity and blunts enhanced length-dependent activation in response to protein kinase A in human cardiomyocytes. Arch Biochem Biophys 2014; 554:11-21. [PMID: 24814372 PMCID: PMC4121669 DOI: 10.1016/j.abb.2014.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
Protein kinase C (PKC)-mediated phosphorylation of troponin I (cTnI) at Ser42/44 is increased in heart failure. While studies in rodents demonstrated that PKC-mediated Ser42/44 phosphorylation decreases maximal force and ATPase activity, PKC incubation of human cardiomyocytes did not affect maximal force. We investigated whether Ser42/44 pseudo-phosphorylation affects force development and ATPase activity using troponin exchange in human myocardium. Additionally, we studied if pseudo-phosphorylated Ser42/44 modulates length-dependent activation of force, which is regulated by protein kinase A (PKA)-mediated cTnI-Ser23/24 phosphorylation. Isometric force was measured in membrane-permeabilized cardiomyocytes exchanged with human recombinant wild-type troponin or troponin mutated at Ser42/44 or Ser23/24 into aspartic acid (D) or alanine (A) to mimic phosphorylation and dephosphorylation, respectively. In troponin-exchanged donor cardiomyocytes experiments were repeated after PKA incubation. ATPase activity was measured in troponin-exchanged cardiac muscle strips. Compared to wild-type, 42D/44D decreased Ca(2+)-sensitivity without affecting maximal force in failing and donor cardiomyocytes. In donor myocardium, 42D/44D did not affect maximal ATPase activity or tension cost. Interestingly, 42D/44D blunted the length-dependent increase in Ca(2+)-sensitivity induced upon PKA-mediated phosphorylation. Since the drop in Ca(2+)-sensitivity at physiological Ca(2+)-concentrations is relatively large phosphorylation of Ser42/44 may result in a decrease of force and associated ATP utilization in the human heart.
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Affiliation(s)
- Paul J M Wijnker
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands; Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Vasco Sequeira
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands.
| | - E Rosalie Witjas-Paalberends
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands.
| | - D Brian Foster
- Department of Pediatrics/Division of Cardiology, Johns Hopkins University School of Medicine, Ross Bldg 1144/720 Rutland Avenue, Baltimore, MD 21205, USA.
| | | | - Anne M Murphy
- Department of Pediatrics/Division of Cardiology, Johns Hopkins University School of Medicine, Ross Bldg 1144/720 Rutland Avenue, Baltimore, MD 21205, USA.
| | - Ger J M Stienen
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands; Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands.
| | - Jolanda van der Velden
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands.
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120
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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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121
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Dweck D, Sanchez-Gonzalez MA, Chang AN, Dulce RA, Badger CD, Koutnik AP, Ruiz EL, Griffin B, Liang J, Kabbaj M, Fincham FD, Hare JM, Overton JM, Pinto JR. Long term ablation of protein kinase A (PKA)-mediated cardiac troponin I phosphorylation leads to excitation-contraction uncoupling and diastolic dysfunction in a knock-in mouse model of hypertrophic cardiomyopathy. J Biol Chem 2014; 289:23097-23111. [PMID: 24973218 DOI: 10.1074/jbc.m114.561472] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cardiac troponin I (cTnI) R21C (cTnI-R21C) mutation has been linked to hypertrophic cardiomyopathy and renders cTnI incapable of phosphorylation by PKA in vivo. Echocardiographic imaging of homozygous knock-in mice expressing the cTnI-R21C mutation shows that they develop hypertrophy after 12 months of age and have abnormal diastolic function that is characterized by longer filling times and impaired relaxation. Electrocardiographic analyses show that older R21C mice have elevated heart rates and reduced cardiovagal tone. Cardiac myocytes isolated from older R21C mice demonstrate that in the presence of isoproterenol, significant delays in Ca(2+) decay and sarcomere relaxation occur that are not present at 6 months of age. Although isoproterenol and stepwise increases in stimulation frequency accelerate Ca(2+)-transient and sarcomere shortening kinetics in R21C myocytes from older mice, they are unable to attain the corresponding WT values. When R21C myocytes from older mice are treated with isoproterenol, evidence of excitation-contraction uncoupling is indicated by an elevation in diastolic calcium that is frequency-dissociated and not coupled to shorter diastolic sarcomere lengths. Myocytes from older mice have smaller Ca(2+) transient amplitudes (2.3-fold) that are associated with reductions (2.9-fold) in sarcoplasmic reticulum Ca(2+) content. This abnormal Ca(2+) handling within the cell may be attributed to a reduction (2.4-fold) in calsequestrin expression in conjunction with an up-regulation (1.5-fold) of Na(+)-Ca(2+) exchanger. Incubation of permeabilized cardiac fibers from R21C mice with PKA confirmed that the mutation prevents facilitation of mechanical relaxation. Altogether, these results indicate that the inability to enhance myofilament relaxation through cTnI phosphorylation predisposes the heart to abnormal diastolic function, reduced accessibility of cardiac reserves, dysautonomia, and hypertrophy.
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Affiliation(s)
- David Dweck
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Marcos A Sanchez-Gonzalez
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300,; Family Institute, Florida State University, Tallahassee, Florida 32306
| | - Audrey N Chang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040
| | - Raul A Dulce
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, and
| | - Crystal-Dawn Badger
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Andrew P Koutnik
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Edda L Ruiz
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Brittany Griffin
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Jingsheng Liang
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida 33136
| | - Mohamed Kabbaj
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Frank D Fincham
- Family Institute, Florida State University, Tallahassee, Florida 32306
| | - Joshua M Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, and
| | - J Michael Overton
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306-4300,.
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122
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Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai W, Chen YC, Guner H, Chen AJ, Schwahn DJ, Hacker TA, Liu X, Ge Y. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Mol Cell Proteomics 2014; 13:2752-64. [PMID: 24969035 PMCID: PMC4189000 DOI: 10.1074/mcp.m114.040675] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality worldwide and is most often precipitated by myocardial infarction. However, the molecular changes driving cardiac dysfunction immediately after myocardial infarction remain poorly understood. Myofilament proteins, responsible for cardiac contraction and relaxation, play critical roles in signal reception and transduction in HF. Post-translational modifications of myofilament proteins afford a mechanism for the beat-to-beat regulation of cardiac function. Thus it is of paramount importance to gain a comprehensive understanding of post-translational modifications of myofilament proteins involved in regulating early molecular events in the post-infarcted myocardium. We have developed a novel liquid chromatography–mass spectrometry-based top-down proteomics strategy to comprehensively assess the modifications of key cardiac proteins in the myofilament subproteome extracted from a minimal amount of myocardial tissue with high reproducibility and throughput. The entire procedure, including tissue homogenization, myofilament extraction, and on-line LC/MS, takes less than three hours. Notably, enabled by this novel top-down proteomics technology, we discovered a concerted significant reduction in the phosphorylation of three crucial cardiac proteins in acutely infarcted swine myocardium: cardiac troponin I and myosin regulatory light chain of the myofilaments and, unexpectedly, enigma homolog isoform 2 (ENH2) of the Z-disc. Furthermore, top-down MS allowed us to comprehensively sequence these proteins and pinpoint their phosphorylation sites. For the first time, we have characterized the sequence of ENH2 and identified it as a phosphoprotein. ENH2 is localized at the Z-disc, which has been increasingly recognized for its role as a nodal point in cardiac signaling. Thus our proteomics discovery opens up new avenues for the investigation of concerted signaling between myofilament and Z-disc in the early molecular events that contribute to cardiac dysfunction and progression to HF.
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Affiliation(s)
- Ying Peng
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Santosh G Valeja
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Han Zhang
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Yi-Chen Chen
- ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Huseyin Guner
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Albert J Chen
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Denise J Schwahn
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Timothy A Hacker
- ‡‡Department of Medicine, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Xiaowen Liu
- §§Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, Indiana 46202; ¶¶Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, Indiana 46202
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706;
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123
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Kooij V, Venkatraman V, Tra J, Kirk JA, Rowell J, Blice-Baum A, Cammarato A, Van Eyk JE. Sizing up models of heart failure: Proteomics from flies to humans. Proteomics Clin Appl 2014; 8:653-64. [PMID: 24723306 PMCID: PMC4282793 DOI: 10.1002/prca.201300123] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/31/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
Abstract
Cardiovascular disease is the leading cause of death in the western world. Heart failure is a heterogeneous and complex syndrome, arising from various etiologies, which result in cellular phenotypes that vary from patient to patient. The ability to utilize genetic manipulation and biochemical experimentation in animal models has made them indispensable in the study of this chronic condition. Similarly, proteomics has been helpful for elucidating complicated cellular and molecular phenotypes and has the potential to identify circulating biomarkers and drug targets for therapeutic intervention. In this review, the use of human samples and animal model systems (pig, dog, rat, mouse, zebrafish, and fruit fly) in cardiac research is discussed. Additionally, the protein sequence homology between these species and the extent of conservation at the level of the phospho-proteome in major kinase signaling cascades involved in heart failure are investigated.
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Affiliation(s)
- Viola Kooij
- Department of Medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, MD, USA
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124
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Effects of hypertension and exercise on cardiac proteome remodelling. BIOMED RESEARCH INTERNATIONAL 2014; 2014:634132. [PMID: 24877123 PMCID: PMC4022191 DOI: 10.1155/2014/634132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/14/2014] [Indexed: 12/29/2022]
Abstract
Left ventricle hypertrophy is a common outcome of pressure overload stimulus closely associated with hypertension. This process is triggered by adverse molecular signalling, gene expression, and proteome alteration. Proteomic research has revealed that several molecular targets are associated with pathologic cardiac hypertrophy, including angiotensin II, endothelin-1 and isoproterenol. Several metabolic, contractile, and stress-related proteins are shown to be altered in cardiac hypertrophy derived by hypertension. On the other hand, exercise is a nonpharmacologic agent used for hypertension treatment, where cardiac hypertrophy induced by exercise training is characterized by improvement in cardiac function and resistance against ischemic insult. Despite the scarcity of proteomic research performed with exercise, healthy and pathologic heart proteomes are shown to be modulated in a completely different way. Hence, the altered proteome induced by exercise is mostly associated with cardioprotective aspects such as contractile and metabolic improvement and physiologic cardiac hypertrophy. The present review, therefore, describes relevant studies involving the molecular characteristics and alterations from hypertensive-induced and exercise-induced hypertrophy, as well as the main proteomic research performed in this field. Furthermore, proteomic research into the effect of hypertension on other target-demerged organs is examined.
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125
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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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126
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Catherman AD, Skinner OS, Kelleher NL. Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun 2014; 445:683-93. [PMID: 24556311 PMCID: PMC4103433 DOI: 10.1016/j.bbrc.2014.02.041] [Citation(s) in RCA: 319] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/10/2014] [Indexed: 12/29/2022]
Abstract
The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
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Affiliation(s)
- Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
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127
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Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch 2014; 466:1199-209. [PMID: 24619480 DOI: 10.1007/s00424-014-1471-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 01/11/2023]
Abstract
The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics--each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
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Chen S, Zhu P, Guo HM, Solis RS, Wang Y, Ma Y, Wang J, Gao J, Chen JM, Ge Y, Zhuang J, Li J. Alpha1 catalytic subunit of AMPK modulates contractile function of cardiomyocytes through phosphorylation of troponin I. Life Sci 2014; 98:75-82. [PMID: 24447627 PMCID: PMC4777330 DOI: 10.1016/j.lfs.2014.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/16/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022]
Abstract
AIMS The specific role of AMPKα1 or AMPKα2 in mediating cardiomyocyte contractile function remains elusive. The present study investigated how AMPK activation modulates the contractility of isolated cardiomyocytes. MAIN METHODS Mechanical properties and intracellular Ca(2+) properties were measured in isolated cardiomyocytes. The stress signaling was evaluated using western blot and immunoprecipitation analysis. KEY FINDINGS AMPK activator, A-769662 induced maximal velocity of shortening (+dL/dt) and relengthening (-dL/dt), peak height and peak shortening (PS) amplitude in both WT and AMPKα2 KO cardiomyocytes, but did not affect time-to-90% relengthening (TR90). AMPK KD cardiomyocytes demonstrated contractile dysfunction compared with cardiomyocytes from WT and AMPKα2 KO hearts. However, the rise of intracellular Ca(2+) levels as well as intracellular ATP levels has no significant difference among WT, AMPKα2 KO and AMPK KD groups with and without the presence of A-769662. Besides, WT, AMPKα2 KO and AMPK KD group displayed a phosphorylated AMPK and downstream acetyl-CoA carboxylase (ACC) phosphorylation. Interestingly, A-769662 also triggered troponin I (cTnI) phosphorylation at Ser(149) site which is related to contractility of cardiomyocytes. Furthermore, the immunoprecipitation analysis revealed that AMPKα1 of cardiomyocytes was phosphorylated by A-769662. SIGNIFICANCE This is the first study illustrating that activation of AMPK plays a significant role in mediating the contractile function of cardiomyocytes using transgenic animal models. AMPK activator facilitates the contractility of cardiomyocytes via activating AMPKα1 catalytic subunit. The phosphorylation of cTnI by AMPK could be a factor attributing to the regulation of contractility of cardiomyocytes.
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Affiliation(s)
- Si Chen
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States
| | - Ping Zhu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hui-Ming Guo
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Raquel Sancho Solis
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, WI, United States
| | - Yanqing Wang
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States
| | - Yina Ma
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States
| | - Jinli Wang
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States
| | - Junjie Gao
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States
| | - Ji-Mei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, WI, United States
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
| | - Ji Li
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo - State University of New York, Buffalo, NY, United States.
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Guner H, Close PL, Cai W, Zhang H, Peng Y, Gregorich ZR, Ge Y. MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:464-70. [PMID: 24385400 PMCID: PMC3940544 DOI: 10.1007/s13361-013-0789-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 05/06/2023]
Abstract
The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.
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Affiliation(s)
- Huseyin Guner
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Patrick L. Close
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Wenxuan Cai
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Han Zhang
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Peng
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Ge
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding author: Dr. Ying Ge, 1300 University Ave., SMI 130, Madison, Wisconsin, USA. Tel: 608-263-9212, Fax: 608-265-5512,
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130
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Milani-Nejad N, Janssen PML. Small and large animal models in cardiac contraction research: advantages and disadvantages. Pharmacol Ther 2014; 141:235-49. [PMID: 24140081 PMCID: PMC3947198 DOI: 10.1016/j.pharmthera.2013.10.007] [Citation(s) in RCA: 308] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/22/2022]
Abstract
The mammalian heart is responsible for not only pumping blood throughout the body but also adjusting this pumping activity quickly depending upon sudden changes in the metabolic demands of the body. For the most part, the human heart is capable of performing its duties without complications; however, throughout many decades of use, at some point this system encounters problems. Research into the heart's activities during healthy states and during adverse impacts that occur in disease states is necessary in order to strategize novel treatment options to ultimately prolong and improve patients' lives. Animal models are an important aspect of cardiac research where a variety of cardiac processes and therapeutic targets can be studied. However, there are differences between the heart of a human being and an animal and depending on the specific animal, these differences can become more pronounced and in certain cases limiting. There is no ideal animal model available for cardiac research, the use of each animal model is accompanied with its own set of advantages and disadvantages. In this review, we will discuss these advantages and disadvantages of commonly used laboratory animals including mouse, rat, rabbit, canine, swine, and sheep. Since the goal of cardiac research is to enhance our understanding of human health and disease and help improve clinical outcomes, we will also discuss the role of human cardiac tissue in cardiac research. This review will focus on the cardiac ventricular contractile and relaxation kinetics of humans and animal models in order to illustrate these differences.
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Affiliation(s)
- Nima Milani-Nejad
- Department of Physiology and Cell Biology and D. Davis Heart Lung Institute, College of Medicine, The Ohio State University, OH, USA
| | - Paul M L Janssen
- Department of Physiology and Cell Biology and D. Davis Heart Lung Institute, College of Medicine, The Ohio State University, OH, USA.
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131
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Wijnker PJM, Sequeira V, Foster DB, Li Y, Dos Remedios CG, Murphy AM, Stienen GJM, van der Velden J. Length-dependent activation is modulated by cardiac troponin I bisphosphorylation at Ser23 and Ser24 but not by Thr143 phosphorylation. Am J Physiol Heart Circ Physiol 2014; 306:H1171-81. [PMID: 24585778 DOI: 10.1152/ajpheart.00580.2013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Frank-Starling's law reflects the ability of the heart to adjust the force of its contraction to changes in ventricular filling, a property based on length-dependent myofilament activation (LDA). The threonine at amino acid 143 of cardiac troponin I (cTnI) is prerequisite for the length-dependent increase in Ca(2+) sensitivity. Thr143 is a known target of protein kinase C (PKC) whose activity is increased in cardiac disease. Thr143 phosphorylation may modulate length-dependent myofilament activation in failing hearts. Therefore, we investigated if pseudo-phosphorylation at Thr143 modulates length dependence of force using troponin exchange experiments in human cardiomyocytes. In addition, we studied effects of protein kinase A (PKA)-mediated cTnI phosphorylation at Ser23/24, which has been reported to modulate LDA. Isometric force was measured at various Ca(2+) concentrations in membrane-permeabilized cardiomyocytes exchanged with recombinant wild-type (WT) troponin or troponin mutated at the PKC site Thr143 or Ser23/24 into aspartic acid (D) or alanine (A) to mimic phosphorylation and dephosphorylation, respectively. In troponin-exchanged donor cardiomyocytes experiments were repeated after incubation with exogenous PKA. Pseudo-phosphorylation of Thr143 increased myofilament Ca(2+) sensitivity compared with WT without affecting LDA in failing and donor cardiomyocytes. Subsequent PKA treatment enhanced the length-dependent shift in Ca(2+) sensitivity after WT and 143D exchange. Exchange with Ser23/24 variants demonstrated that pseudo-phosphorylation of both Ser23 and Ser24 is needed to enhance the length-dependent increase in Ca(2+) sensitivity. cTnI pseudo-phosphorylation did not alter length-dependent changes in maximal force. Thus phosphorylation at Thr143 enhances myofilament Ca(2+) sensitivity without affecting LDA, while Ser23/24 bisphosphorylation is needed to enhance the length-dependent increase in myofilament Ca(2+) sensitivity.
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Affiliation(s)
- Paul J M Wijnker
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands
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Efficient separations of intact proteins using slip-flow with nano-liquid chromatography-mass spectrometry. Anal Chem 2014; 86:1592-8. [PMID: 24383398 PMCID: PMC3982985 DOI: 10.1021/ac403233d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
A capillary with a pulled tip, densely
packed with silica particles
of 0.47 μm in diameter, is shown to provide higher peak capacity
and sensitivity in the separation of intact proteins by reversed-phase
liquid chromatography–mass spectrometry (LC–MS). For
a C18 bonded phase, slip flow gave a 10-fold flow enhancement to allow
for stable nanospray with a 4-cm column length. Model proteins were
studied: ribonuclease A, trypsin inhibitor, and carbonic anhydrase,
where the latter had impurities of superoxide dismutase and ubiquitin.
The proteins were well separated at room temperature with negligible
peak tailing. The peak capacity for ubiquitin was 195 for a 10-min
gradient and 315 for a 40-min gradient based on Gaussian fitting of
the entire peak, rather than extrapolating the full-width at half-maximum.
Separation of a cell lysate with a 60 min gradient showed extremely
high peak capacities of 750 and above for a peptide and relatively
homogeneous proteins. Clean, low noise mass spectra for each model
protein were obtained. The physical widths of the peaks were an order
of magnitude narrower than those of conventional columns, giving increased
sensitivity. All proteins except ubiquitin exhibited significant heterogeneity
apparently due to multiple proteoforms, as indicated by both peak
shapes and mass spectra. The chromatograms exhibited excellent reproducibility
in retention time, with relative standard deviations of 0.09 to 0.34%.
The results indicate that submicrometer particles are promising for
improving the separation dimension of LC in top-down proteomics.
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133
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Katrukha IA. Human cardiac troponin complex. Structure and functions. BIOCHEMISTRY (MOSCOW) 2014; 78:1447-65. [DOI: 10.1134/s0006297913130063] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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134
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Zong NC, Li H, Li H, Lam MPY, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P. Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circ Res 2013; 113:1043-53. [PMID: 23965338 DOI: 10.1161/circresaha.113.301151] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. OBJECTIVE The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. METHODS AND RESULTS We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. CONCLUSIONS COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.
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Affiliation(s)
- Nobel C Zong
- From the NHLBI Proteomics Center at UCLA/NHLBI Proteomics Program
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135
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Taube D, Xu J, Yang XP, Undrovinas A, Peterson E, Harding P. Fractalkine depresses cardiomyocyte contractility. PLoS One 2013; 8:e69832. [PMID: 23936109 PMCID: PMC3728327 DOI: 10.1371/journal.pone.0069832] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/14/2013] [Indexed: 12/02/2022] Open
Abstract
Background Our laboratory reported that male mice with cardiomyocyte-selective knockout of the prostaglandin E2 EP4 receptor sub-type (EP4 KO) exhibit reduced cardiac function. Gene array on left ventricles (LV) showed increased fractalkine, a chemokine implicated in heart failure. We therefore hypothesized that fractalkine is regulated by PGE2 and contributes to depressed contractility via alterations in intracellular calcium. Methods Fractalkine was measured in LV of 28–32 week old male EP4 KO and wild type controls (WT) by ELISA and the effect of PGE2 on fractalkine secretion was measured in cultured neonatal cardiomyocytes and fibroblasts. The effect of fractalkine on contractility and intracellular calcium was determined in Fura-2 AM-loaded, electrical field-paced cardiomyocytes. Cardiomyocytes (AVM) from male C57Bl/6 mice were treated with fractalkine and responses measured under basal conditions and after isoproterenol (Iso) stimulation. Results LV fractalkine was increased in EP4 KO mice but surprisingly, PGE2 regulated fractalkine secretion only in fibroblasts. Fractalkine treatment of AVM decreased both the speed of contraction and relaxation under basal conditions and after Iso stimulation. Despite reducing contractility after Iso stimulation, fractalkine increased the Ca2+ transient amplitude but decreased phosphorylation of cardiac troponin I, suggesting direct effects on the contractile machinery. Conclusions Fractalkine depresses myocyte contractility by mechanisms downstream of intracellular calcium.
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Affiliation(s)
- David Taube
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Jiang Xu
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Xiao-Ping Yang
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Albertas Undrovinas
- Cardiovascular Research Division, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Edward Peterson
- Department of Internal Medicine and Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Pamela Harding
- Hypertension and Vascular Research Division, Henry Ford Hospital, Detroit, Michigan, United States of America
- * E-mail:
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136
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In-depth proteomic analysis of human tropomyosin by top-down mass spectrometry. J Muscle Res Cell Motil 2013; 34:199-210. [PMID: 23881156 DOI: 10.1007/s10974-013-9352-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/27/2013] [Indexed: 01/29/2023]
Abstract
Tropomyosins (Tms) are a family of highly conserved actin-binding proteins that play critical roles in a variety of processes, most notably, in the regulation of muscle contraction and relaxation. It is well known that different Tm isoforms have distinct functions and that altered expression of Tm isoforms could lead to changes in cardiac structure and function. To precisely define Tm isoform expression in the human heart, towards a better understanding of their functional roles, we have employed top-down mass spectrometry for in-depth proteomic characterization of Tm isoforms. Using a minimal amount of human heart tissue from rejected donor organs, we confirmed the presence of multiple Tm isoforms including α-Tm, β-Tm and κ-Tm in the human heart, with α-Tm being the predominant isoform, followed by minor isoforms of β-Tm and κ-Tm. Interestingly, our data revealed regional variations of Tm isoforms and post-translational modifications in the human heart. Specifically, the expression level of κ-Tm was highest in the left atrium but nearly undetectable in the left ventricle. The phosphorylation level of α-Tm (pα-Tm) was significantly higher in the atria than it was in the ventricles. The sequences of all Tm isoforms were characterized and the sites of post-translational modifications were localized. Clearly, top-down mass spectrometry is an attractive method for comprehensive characterization of Tm isoforms and post-translational modifications since it can universally detect and quantify all types of protein modifications without a priori knowledge and without the need for specific antibodies.
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137
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Liu X, Jin Z, O’Brien R, Bathon J, Dietz HC, Grote E, Van Eyk JE. Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms. Methods 2013; 61:304-12. [PMID: 23523700 PMCID: PMC3990191 DOI: 10.1016/j.ymeth.2013.03.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/02/2013] [Accepted: 03/06/2013] [Indexed: 10/27/2022] Open
Abstract
Selected reaction monitoring (SRM) is a mass spectrometry method that can target signature peptides to provide for the detection and quantitation of specific proteins in complex biological samples. When quantifying a protein, multiple peptides are generated using a specific protease such as trypsin, thereby allowing a choice of signature peptides with robust signals. In contrast, signature peptide selection can be constrained when the goal is to monitor a specific post-translational modification (PTM) or protein isoform, as the signature peptide must include the amino acid residue(s) of PTM attachment or sequence variation. This can force the selection of a signature peptide with a weak SRM response or one that is confounded by high background. In this article, we discuss steps that can be optimized to maximize peptide selection and assay performance of constrained SRM assays, including tuning instrument parameters, fragmenting product ions, using a different protease, and enriching the sample. Examples are provided for phosphorylated or citrullinated peptides and protein isoforms.
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Affiliation(s)
- Xiaoqian Liu
- Department of Medicine, Jonhns Hopkins University, New York, NY
| | - Zhicheng Jin
- Department of Medicine, Jonhns Hopkins University, New York, NY
| | - Richard O’Brien
- Department of Neurology, Johns Hopkins Bayview Medical Center, New York, NY
| | - Joan Bathon
- Department of Medicine, Columbia Medical School, New York, NY
| | - Harry C. Dietz
- Department of Pediatrics, Johns Hopkins University, Baltimore MD
| | - Eric Grote
- Department of Medicine, Jonhns Hopkins University, New York, NY
| | - Jennifer E. Van Eyk
- Department of Medicine, Jonhns Hopkins University, New York, NY
- Department of Biological Chemistry and Biomedical Engineering, Johns Hopkins University, Baltimore MD
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Yoneyama T, Ohtsuki S, Ono M, Ohmine K, Uchida Y, Yamada T, Tachikawa M, Terasaki T. Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated α-fibrinogen in plasma for pancreatic cancer diagnosis. J Proteome Res 2013; 12:753-62. [PMID: 23298340 DOI: 10.1021/pr3008144] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pancreatic cancer is a devastating disease and early diagnosis and treatment are essential to improve the prognosis. We previously showed that α-fibrinogen containing hydroxylated proline residues at positions 530 and 565 is increased in plasma of pancreatic cancer patients. However, no antibody specific for hydroxylated proline-530 is available. Therefore, the purposes of this study were to develop a quantification method specific for both proline-hydroxylated α-fibrinogens by selected/multiple reaction monitoring (SRM/MRM), and to validate these modifications as pancreatic cancer markers. The target peptide for hydroxylated proline-530 contained methionine, and since variable partial oxidation of this residue would affect the quantification, hydrogen peroxide treatment was carried out to ensure complete oxidation. Quantification values of modified and unmodified α-fibrinogen were well correlated with those obtained by immunoblotting. Concentrations of modified and unmodified α-fibrinogen were quantified in 70 pancreatic cancer patients and 27 healthy controls. Percent hydroxylation of α-fibrinogen and concentration of hydroxylated α-fibrinogen were significantly greater in the plasma of patients. Furthermore, among 8 carbohydrate antigen 19-9 (CA19-9)-negative patients in stages I/II, 6 were positive for proline-hydroxylated α-fibrinogen. These results indicate that plasma concentration of proline-hydroxylated α-fibrinogen measured by SRM/MRM analysis may be a good pancreatic cancer marker, especially in CA19-9-negative patients.
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Affiliation(s)
- Toshihiro Yoneyama
- Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba, Aramaki, Sendai 980-8578, Japan
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139
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Peng Y, Chen X, Zhang H, Xu Q, Hacker TA, Ge Y. Top-down targeted proteomics for deep sequencing of tropomyosin isoforms. J Proteome Res 2013; 12:187-98. [PMID: 23256820 PMCID: PMC3596867 DOI: 10.1021/pr301054n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Tropomyosins (Tm) constitute a family of ubiquitous and highly conserved actin-binding proteins, playing essential roles in a variety of biological processes. Tm isoforms produced by multiple Tm encoding genes and alternatively expressed exons along with post-translational modifications (PTMs) regulate Tm function. Therefore, to gain a better understanding of the functional role of Tm, it is essential to fully characterize Tm isoforms. Herein, we developed a top-down high-resolution mass spectrometry (MS)-based targeted proteomics method for comprehensive characterization of Tm isoforms. α-Tm was identified to be the predominant isoform in swine cardiac muscle. We further characterized its sequence and localized the PTMs such as acetylation and phosphorylation as well as amino acid polymorphisms. Interestingly, we discovered a "novel" Tm isoform that does not match with any of the currently available swine Tm sequences. A deep sequencing of this isoform by top-down MS revealed an exact match with mouse β-Tm sequence, suggesting that this "novel" isoform is swine β-Tm which is 100% conserved between swine and mouse. Taken together, we demonstrated that top-down targeted proteomics provides a powerful tool for deep sequencing of Tm isoforms from genetic variations together with complete mapping of the PTM sites.
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Affiliation(s)
- Ying Peng
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
| | - Xin Chen
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
| | - Han Zhang
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Qingge Xu
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
| | - Timothy A. Hacker
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
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140
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Recent advances in cardiovascular proteomics. J Proteomics 2012; 81:3-14. [PMID: 23153792 DOI: 10.1016/j.jprot.2012.10.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 10/10/2012] [Accepted: 10/31/2012] [Indexed: 01/08/2023]
Abstract
Cardiovascular diseases (CVDs) are the major source of global morbidity and death and more people die annually from CVDs than from any other cause. These diseases can occur quickly, as seen in acute myocardial infarction (AMI), or progress slowly over years as with chronic heart failure. Advances in mass spectrometry detection and analysis, together with improved isolation and enrichment techniques allowing for the separation of organelles and membrane proteins, now allow for the indepth analysis of the cardiac proteome. Here we outline current insights that have been provided through cardiovascular proteomics, and discuss studies that have developed innovative technologies which permit the examination of the protein complement in specific organelles including exosomes and secreted proteins. We highlight these foundational studies and illustrate how they are providing the technologies and tools which are now being applied to further study cardiovascular disease; provide new diagnostic markers and potentially new methods of cardiac patient management with identification of novel drug targets. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Wijnker PJM, Foster DB, Tsao AL, Frazier AH, dos Remedios CG, Murphy AM, Stienen GJM, van der Velden J. Impact of site-specific phosphorylation of protein kinase A sites Ser23 and Ser24 of cardiac troponin I in human cardiomyocytes. Am J Physiol Heart Circ Physiol 2012; 304:H260-8. [PMID: 23144315 DOI: 10.1152/ajpheart.00498.2012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PKA-mediated phosphorylation of contractile proteins upon β-adrenergic stimulation plays an important role in the regulation of cardiac performance. Phosphorylation of the PKA sites (Ser(23)/Ser(24)) of cardiac troponin (cTn)I results in a decrease in myofilament Ca(2+) sensitivity and an increase in the rate of relaxation. However, the relation between the level of phosphorylation of the sites and the functional effects in the human myocardium is unknown. Therefore, site-directed mutagenesis was used to study the effects of phosphorylation at Ser(23) and Ser(24) of cTnI on myofilament function in human cardiac tissue. Serines were replaced by aspartic acid (D) or alanine (A) to mimic phosphorylation and dephosphorylation, respectively. cTnI-DD mimics both sites phosphorylated, cTnI-AD mimics Ser(23) unphosphorylated and Ser(24) phosphorylated, cTnI-DA mimics Ser(23) phosphorylated and Ser(24) unphosphorylated, and cTnI-AA mimics both sites unphosphorylated. Force development was measured at various Ca(2+) concentrations in permeabilized cardiomyocytes in which the endogenous troponin complex was exchanged with these recombinant human troponin complexes. In donor cardiomyocytes, myofilament Ca(2+) sensitivity (pCa(50)) was significantly lower in cTnI-DD (pCa(50): 5.39 ± 0.01) compared with cTnI-AA (pCa(50): 5.50 ± 0.01), cTnI-AD (pCa(50): 5.48 ± 0.01), and cTnI-DA (pCa(50): 5.51 ± 0.01) at ~70% cTn exchange. No effects were observed on the rate of tension redevelopment. In cardiomyocytes from idiopathic dilated cardiomyopathic tissue, a linear decline in pCa(50) with cTnI-DD content was observed, saturating at ~55% bisphosphorylation. Our data suggest that in the human myocardium, phosphorylation of both PKA sites on cTnI is required to reduce myofilament Ca(2+) sensitivity, which is maximal at ~55% bisphosphorylated cTnI. The implications for in vivo cardiac function in health and disease are detailed in the DISCUSSION in this article.
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Affiliation(s)
- Paul J M Wijnker
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands.
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142
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Guy MJ, Chen YC, Clinton L, Zhang H, Zhang J, Dong X, Xu Q, Ayaz-Guner S, Ge Y. The impact of antibody selection on the detection of cardiac troponin I. Clin Chim Acta 2012; 420:82-8. [PMID: 23107929 DOI: 10.1016/j.cca.2012.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 10/17/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cardiac troponin I (cTnI) is the current standard biomarker for diagnosing acute myocardial infarction and for risk-stratification of acute coronary syndromes in patients. However, it remains unclear how the epitope specificity of antibodies in immunoassays influences the detection of various modified forms of cTnI. METHODS Four mouse anti-human cTnI monoclonal antibodies targeting different regions of human cTnI were chosen for immunoaffinity purification of cTnI from human and swine cardiac tissue. High-resolution intact protein mass spectrometry was employed to assess the comparative performance of these four antibodies in detecting modified forms of cTnI. RESULTS Our data revealed that antibody selection significantly impacts the relative protein yield of cTn from immunoaffinity purification. Remarkably, a single amino acid variation in cTnI (G->S) in the epitope region completely abolished the binding between monoclonal antibody 560 and swine cTnI in solution. Moreover, proteolytic degradation around the epitope region severely compromised the detection of proteolytic fragment forms of cTnI by monoclonal antibodies. In contrast, the phosphorylation status near the epitope region did not significantly affect the antibody recognition of cTnI. CONCLUSION Caution needs to be taken in the interpretation of the data produced by immuno-assays with monoclonal antibodies against various epitopes of cTnI.
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Affiliation(s)
- Moltu J Guy
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, United States
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143
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Zhang P, Kirk JA, Ji W, dos Remedios CG, Kass DA, Van Eyk JE, Murphy AM. Multiple reaction monitoring to identify site-specific troponin I phosphorylated residues in the failing human heart. Circulation 2012; 126:1828-37. [PMID: 22972900 DOI: 10.1161/circulationaha.112.096388] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Human cardiac troponin I is known to be phosphorylated at multiple amino acid residues by several kinases. Advances in mass spectrometry allow sensitive detection of known and novel phosphorylation sites and measurement of the level of phosphorylation simultaneously at each site in myocardial samples. METHODS AND RESULTS On the basis of in silico prediction and liquid chromatography/mass spectrometry data, 14 phosphorylation sites on cardiac troponin I, including 6 novel residues (S4, S5, Y25, T50, T180, S198), were assessed in explanted hearts from end-stage heart failure transplantation patients with ischemic heart disease or idiopathic dilated cardiomyopathy and compared with samples obtained from nonfailing donor hearts (n=10 per group). Thirty mass spectrometry-based multiple reaction monitoring quantitative tryptic peptide assays were developed for each phosphorylatable and corresponding nonphosphorylated site. The results show that in heart failure there is a decrease in the extent of phosphorylation of the known protein kinase A sites (S22, S23) and other newly discovered phosphorylation sites located in the N-terminal extension of cardiac troponin I (S4, S5, Y25), an increase in phosphorylation of the protein kinase C sites (S41, S43, T142), and an increase in phosphorylation of the IT-arm domain residues (S76, T77) and C-terminal domain novel phosphorylation sites of cardiac troponin I (S165, T180, S198). In a canine dyssynchronous heart failure model, enhanced phosphorylation at 3 novel sites was found to decline toward control after resynchronization therapy. CONCLUSIONS Selective, functionally significant phosphorylation alterations occurred on individual residues of cardiac troponin I in heart failure, likely reflecting an imbalance in kinase/phosphatase activity. Such changes can be reversed by cardiac resynchronization.
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Affiliation(s)
- Pingbo Zhang
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
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144
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Human myocardial protein pattern reveals cardiac diseases. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:342659. [PMID: 22928107 PMCID: PMC3423942 DOI: 10.1155/2012/342659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 03/28/2012] [Indexed: 11/17/2022]
Abstract
Proteomic profiles of myocardial tissue in two different etiologies of heart failure were investigated using high performance liquid chromatography (HPLC)/Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Right atrial appendages from 10 patients with hemodynamically significant isolated aortic valve disease and from 10 patients with isolated symptomatic coronary heart disease were collected during elective cardiac surgery. As presented in an earlier study by our group (Baykut et al., 2006), both disease forms showed clearly different pattern distribution characteristics. Interesting enough, the classification patterns could be used for correctly sorting unknown test samples in their correct categories. However, in order to fully exploit and also validate these findings there is a definite need for unambiguous identification of the differences between different etiologies at molecular level. In this study, samples representative for the aortic valve disease and coronary heart disease were prepared, tryptically digested, and analyzed using an FT-ICR MS that allowed collision-induced dissociation (CID) of selected classifier masses. By using the fragment spectra, proteins were identified by database searches. For comparison and further validation, classifier masses were also fragmented and analyzed using HPLC-/Matrix-assisted laser desorption ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry. Desmin and lumican precursor were examples of proteins found in aortic samples at higher abundances than in coronary samples. Similarly, adenylate kinase isoenzyme was found in coronary samples at a higher abundance. The described methodology could also be feasible in search for specific biomarkers in plasma or serum for diagnostic purposes.
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145
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Su JB, Cazorla O, Blot S, Blanchard-Gutton N, Ait Mou Y, Barthélémy I, Sambin L, Sampedrano CC, Gouni V, Unterfinger Y, Aguilar P, Thibaud JL, Bizé A, Pouchelon JL, Dabiré H, Ghaleh B, Berdeaux A, Chetboul V, Lacampagne A, Hittinger L. Bradykinin restores left ventricular function, sarcomeric protein phosphorylation, and e/nNOS levels in dogs with Duchenne muscular dystrophy cardiomyopathy. Cardiovasc Res 2012; 95:86-96. [PMID: 22562664 DOI: 10.1093/cvr/cvs161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIMS Cardiomyopathy is a lethal result of Duchenne muscular dystrophy (DMD), but its characteristics remain elusive. The golden retriever muscular dystrophy (GRMD) dogs produce DMD pathology and mirror DMD patient's symptoms, including cardiomyopathy. We previously showed that bradykinin slows the development of pacing-induced heart failure. Therefore, the goals of this research were to characterize dystrophin-deficiency cardiomyopathy and to examine cardiac effects of bradykinin in GRMD dogs. METHODS AND RESULTS At baseline, adult GRMD dogs had reduced fractional shortening (28 ± 2 vs. 38 ± 2% in control dogs, P < 0.001) and left ventricular (LV) subendocardial dysfunction leading to impaired endo-epicardial gradient of radial systolic velocity (1.3 ± 0.1 vs. 3.8 ± 0.2 cm/s in control dogs, P < 0.001) measured by echocardiography. These changes were normalized by bradykinin infusion (1 µg/min, 4 weeks). In isolated permeabilized LV subendocardial cells of GRMD dogs, tension-calcium relationships were shifted downward and force-generating capacity and transmural gradient of myofilament length-dependent activation were impaired compared with control dogs. Concomitantly, phosphorylation of sarcomeric regulatory proteins and levels of endothelial and neuronal nitric oxide synthase (e/nNOS) in LV myocardium were significantly altered in GRMD dogs. All these abnormalities were normalized in bradykinin-treated GRMD dogs. CONCLUSIONS Cardiomyopathy in GRMD dogs is characterized by profound LV subendocardial dysfunction, abnormal sarcomeric protein phosphorylation, and impaired e/nNOS, which can be normalized by bradykinin treatment. These data provide new insights into the pathophysiological mechanisms accounting for DMD cardiomyopathy and open new therapeutic perspectives.
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Affiliation(s)
- Jin Bo Su
- INSERM U955, ENVA, 7 avenu du Général de Gaulle, Maisons-Alfort, France.
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146
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Peng Y, Chen X, Sato T, Rankin SA, Tsuji RF, Ge Y. Purification and high-resolution top-down mass spectrometric characterization of human salivary α-amylase. Anal Chem 2012; 84:3339-46. [PMID: 22390166 DOI: 10.1021/ac300083y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human salivary α-amylase (HSAMY) is a major component of salivary secretions, possessing multiple important biological functions. Here we have established three methods to purify HSAMY in human saliva for comprehensive characterization of HSAMY by high-resolution top-down mass spectrometry (MS). Among the three purification methods, the affinity method based on the enzyme-substrate specific interaction between amylase and glycogen is preferred, providing the highest purity HSAMY with high reproducibility. Subsequently, we employed Fourier transform ion cyclotron resonance MS to analyze the purified HSAMY. The predominant form of α-amylase purified from saliva of various races and genders is nonglycosylated with the same molecular weight of 55,881.2, which is 1885.8 lower than the calculated value based on the DNA-predicted sequence. High-resolution MS revealed the truncation of the first 15 N-terminal amino acids (-1858.96) and the subsequent formation of pyroglutamic acid at the new N-terminus Gln (-17.03). More importantly, five disulfide bonds in HSAMY were identified (-10.08) and effectively localized by tandem MS in conjunction with complete and partial reduction by tris (2-carboxyethyl) phosphine. Overall, this study demonstrates that top-down MS combined with affinity purification and partial reduction is a powerful method for rapid purification and complete characterization of large proteins with complex and overlapping disulfide bond patterns.
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Affiliation(s)
- Ying Peng
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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147
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Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
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Wang Y, Pinto JR, Solis RS, Dweck D, Liang J, Diaz-Perez Z, Ge Y, Walker JW, Potter JD. Generation and functional characterization of knock-in mice harboring the cardiac troponin I-R21C mutation associated with hypertrophic cardiomyopathy. J Biol Chem 2011; 287:2156-67. [PMID: 22086914 DOI: 10.1074/jbc.m111.294306] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R21C substitution in cardiac troponin I (cTnI) is the only identified mutation within its unique N-terminal extension that is associated with hypertrophic cardiomyopathy (HCM) in man. Particularly, this mutation is located in the consensus sequence for β-adrenergic-activated protein kinase A (PKA)-mediated phosphorylation. The mechanisms by which this mutation leads to heart disease are still unclear. Therefore, we generated cTnI knock-in mouse models carrying an R21C mutation to evaluate the resultant functional consequences. Measuring the in vivo levels of incorporated mutant and WT cTnI, and their basal phosphorylation levels by top-down mass spectrometry demonstrated: 1) a dominant-negative effect such that, the R21C+/- hearts incorporated 24.9% of the mutant cTnI within the myofilament; and 2) the R21C mutation abolished the in vivo phosphorylation of Ser(23)/Ser(24) in the mutant cTnI. Adult heterozygous (R21C+/-) and homozygous (R21C+/+) mutant mice activated the fetal gene program and developed a remarkable degree of cardiac hypertrophy and fibrosis. Investigation of cardiac skinned fibers isolated from WT and heterozygous mice revealed that the WT cTnI was completely phosphorylated at Ser(23)/Ser(24) unless the mice were pre-treated with propranolol. After propranolol treatment (-PKA), the pCa-tension relationships of all three mice (i.e. WT, R21C+/-, and R21C+/+) were essentially the same. However, after treatment with propranolol and PKA, the R21C cTnI mutation reduced (R21C+/-) or abolished (R21C+/+) the well known decrease in the Ca(2+) sensitivity of tension that accompanies Ser(23)/Ser(24) cTnI phosphorylation. Altogether, the combined effects of the R21C mutation appear to contribute toward the development of HCM and suggest that another physiological role for the phosphorylation of Ser(23)/Ser(24) in cTnI is to prevent cardiac hypertrophy.
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Affiliation(s)
- Yingcai Wang
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, Florida 33136, USA
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149
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Dong X, Sumandea CA, Chen YC, Garcia-Cazarin ML, Zhang J, Balke CW, Sumandea MP, Ge Y. Augmented phosphorylation of cardiac troponin I in hypertensive heart failure. J Biol Chem 2011; 287:848-57. [PMID: 22052912 DOI: 10.1074/jbc.m111.293258] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An altered cardiac myofilament response to activating Ca(2+) is a hallmark of human heart failure. Phosphorylation of cardiac troponin I (cTnI) is critical in modulating contractility and Ca(2+) sensitivity of cardiac muscle. cTnI can be phosphorylated by protein kinase A (PKA) at Ser(22/23) and protein kinase C (PKC) at Ser(22/23), Ser(42/44), and Thr(143). Whereas the functional significance of Ser(22/23) phosphorylation is well understood, the role of other cTnI phosphorylation sites in the regulation of cardiac contractility remains a topic of intense debate, in part, due to the lack of evidence of in vivo phosphorylation. In this study, we utilized top-down high resolution mass spectrometry (MS) combined with immunoaffinity chromatography to determine quantitatively the cTnI phosphorylation changes in spontaneously hypertensive rat (SHR) model of hypertensive heart disease and failure. Our data indicate that cTnI is hyperphosphorylated in the failing SHR myocardium compared with age-matched normotensive Wistar-Kyoto rats. The top-down electron capture dissociation MS unambiguously localized augmented phosphorylation sites to Ser(22/23) and Ser(42/44) in SHR. Enhanced Ser(22/23) phosphorylation was verified by immunoblotting with phospho-specific antibodies. Immunoblot analysis also revealed up-regulation of PKC-α and -δ, decreased PKCε, but no changes in PKA or PKC-β levels in the SHR myocardium. This provides direct evidence of in vivo phosphorylation of cTnI-Ser(42/44) (PKC-specific) sites in an animal model of hypertensive heart failure, supporting the hypothesis that PKC phosphorylation of cTnI may be maladaptive and potentially associated with cardiac dysfunction.
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Affiliation(s)
- Xintong Dong
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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