1
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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2
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Gong M, Zhang Y, Chen N, Ma LL, Feng XM, Yan YX. Proteomics in Cardiovascular disease. Clin Chim Acta 2024; 557:117877. [PMID: 38537675 DOI: 10.1016/j.cca.2024.117877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
This study focuses on recent advances in proteomics and provides an up-to-date use of this technology in identifying cardiovascular disease (CVD) biomarkers. A total of eight electronic databases (PubMed, EMBASE, Web of Science, Cochrane Library, Wanfang, Vip, Sinomed, and CNKI) were searched and five were used for integrative analysis of sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic ratio (DOR) and 1 secondary indicator area under the curve (AUC). This systematic review and integrative analysis summarized potential biomarkers previously identified by proteomics. The integrative analysis suggested that proteomics technology had high clinical value in CVD diagnosis. The findings provided new possible directions for the prevention or diagnosis of CVD.
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Affiliation(s)
- Miao Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Yu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Ning Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Lin-Lin Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Xu-Man Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Yu-Xiang Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China; Municipal Key Laboratory of Clinical Epidemiology, Beijing, China.
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3
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Mota GAF, de Souza SLB, Vileigas DF, da Silva VL, Sant'Ana PG, Costa LCDS, Padovani CR, Zanatti Bazan SG, Buzalaf MAR, Santos LDD, Okoshi MP, Gatto M, Cicogna AC. Myocardial proteome changes in aortic stenosis rats subjected to long-term aerobic exercise. J Cell Physiol 2024; 239:e31199. [PMID: 38291668 DOI: 10.1002/jcp.31199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
The effects of exercise training (ET) on the heart of aortic stenosis (AS) rats are controversial and the mechanisms involved in alterations induced by ET have been poorly clarified. In this study, we analyzed the myocardial proteome to identify proteins modulated by moderate-intensity aerobic ET in rats with chronic supravalvular AS. Wistar rats were divided into four groups: sedentary control (C-Sed), exercised control (C-Ex), sedentary aortic stenosis (AS-Sed), and exercised AS (AS-Ex). ET consisted of five treadmill running sessions per week for 16 weeks. Statistical analysis was performed by ANOVA or Kruskal-Wallis and Goodman tests. Results were discussed at a significance level of 5%. At the end of the experiment, AS-Ex rats had higher functional capacity, lower blood lactate concentration, and better cardiac structural and left ventricular (LV) functional parameters than the AS-Sed. Myocardial proteome analysis showed that AS-Sed had higher relative protein abundance related to the glycolytic pathway, oxidative stress, and inflammation, and lower relative protein abundance related to beta-oxidation than C-Sed. AS-Ex had higher abundance of one protein related to mitochondrial biogenesis and lower relative protein abundance associated with oxidative stress and inflammation than AS-Sed. Proteomic data were validated for proteins related to lipid and glycolytic metabolism. Chronic pressure overload changes the abundance of myocardial proteins that are mainly involved in lipid and glycolytic energy metabolism in rats. Moderate-intensity aerobic training attenuates changes in proteins related to oxidative stress and inflammation and increases the COX4I1 protein, related to mitochondrial biogenesis. Protein changes are combined with improved functional capacity, cardiac remodeling, and LV function in AS rats.
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Affiliation(s)
- Gustavo Augusto Ferreira Mota
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Sérgio Luiz Borges de Souza
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | | | - Vitor Loureiro da Silva
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Paula Grippa Sant'Ana
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Licia Carla da Silva Costa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, São Paulo, Brazil
| | - Carlos Roberto Padovani
- Department of Biostatistics, Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Silméia Garcia Zanatti Bazan
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | | | | | - Marina Politi Okoshi
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Mariana Gatto
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
| | - Antonio Carlos Cicogna
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University, UNESP, São Paulo, São Paulo, Brazil
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4
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Ai L, Binek A, Kreimer S, Ayres M, Stotland A, Van Eyk JE. High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing. J Proteome Res 2023; 22:2124-2130. [PMID: 37040897 PMCID: PMC10243111 DOI: 10.1021/acs.jproteome.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 04/13/2023]
Abstract
Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.
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Affiliation(s)
- Lizhuo Ai
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Simion Kreimer
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandr Stotland
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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5
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Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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6
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Zhao X, Xu H, Li Y, Ma R, Qi Y, Zhang M, Guo C, Sun Z, Li Y. Proteomic profiling reveals dysregulated mitochondrial complex subunits responsible for myocardial toxicity induced by SiNPs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159206. [PMID: 36198348 DOI: 10.1016/j.scitotenv.2022.159206] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
The relationship between environmental exposure to silica nanoparticles (SiNPs) and adverse cardiac outcomes has received more attention. Our recent work has revealed a size-dependent impact of the intratracheal instilled SiNPs on cardiac health of ApoE-/- mice using nanoscale SiNPs-60 and submicro-sized SiNPs-300, but the underlying mechanism of action still remains unclear. Hence, we identified proteins and protein networks perturbed by SiNPs in myocardial tissues of ApoE-/- mice by using LC-MS/MS-based quantitative proteomics. A set of 435 differentially expressed proteins (DEPs) were screened in response to SiNPs, which mainly enriched in the mitochondria and functioned in cell metabolism, biosynthesis and signal transduction. KEGG analysis showed that DEPs were significantly associated with oxidative phosphorylation and cardiomyopathy. The protein-protein interaction (PPI) network revealed 9 DEPs (e.g., Ndufs1, Ndufv1, Cox4i1) as potential biomarkers of SiNPs-induced myocardial toxicity. Of note, all the 9 candidate proteins were subunits of mitochondria respiratory chain complex, and their expressions were dependent on particle size, which were remarkably down-regulated by SiNPs-60 but not by SiNPs-300. More importantly, the correlation analysis verified the 9 dysregulated mitochondria complex protein subunits strongly correlated to the biochemical and functional indexes of cardiac injury in response to SiNPs. In conclusion, our study firstly provided significant proteomic insights into the potential molecular mechanisms underlying SiNPs-elicited cardiotoxicity, with the dysregulated mitochondrial complex subunits as core regulatory molecules. Overall, our study would provide the scientific basis for the molecular actions and mechanisms of toxicity induced by SiNPs.
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Affiliation(s)
- Xinying Zhao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Hailin Xu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yan Li
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Ru Ma
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yi Qi
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Min Zhang
- Department of Nephrology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Caixia Guo
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yanbo Li
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
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7
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Teixeira PC, Ducret A, Langen H, Nogoceke E, Santos RHB, Silva Nunes JP, Benvenuti L, Levy D, Bydlowski SP, Bocchi EA, Kuramoto Takara A, Fiorelli AI, Stolf NA, Pomeranzeff P, Chevillard C, Kalil J, Cunha-Neto E. Impairment of Multiple Mitochondrial Energy Metabolism Pathways in the Heart of Chagas Disease Cardiomyopathy Patients. Front Immunol 2021; 12:755782. [PMID: 34867990 PMCID: PMC8633876 DOI: 10.3389/fimmu.2021.755782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
Chagas disease cardiomyopathy (CCC) is an inflammatory dilated cardiomyopathy occurring in 30% of the 6 million infected with the protozoan Trypanosoma cruzi in Latin America. Survival is significantly lower in CCC than ischemic (IC) and idiopathic dilated cardiomyopathy (DCM). Previous studies disclosed a selective decrease in mitochondrial ATP synthase alpha expression and creatine kinase activity in CCC myocardium as compared to IDC and IC, as well as decreased in vivo myocardial ATP production. Aiming to identify additional constraints in energy metabolism specific to CCC, we performed a proteomic study in myocardial tissue samples from CCC, IC and DCM obtained at transplantation, in comparison with control myocardial tissue samples from organ donors. Left ventricle free wall myocardial samples were subject to two-dimensional electrophoresis with fluorescent labeling (2D-DIGE) and protein identification by mass spectrometry. We found altered expression of proteins related to mitochondrial energy metabolism, cardiac remodeling, and oxidative stress in the 3 patient groups. Pathways analysis of proteins differentially expressed in CCC disclosed mitochondrial dysfunction, fatty acid metabolism and transmembrane potential of mitochondria. CCC patients’ myocardium displayed reduced expression of 22 mitochondrial proteins belonging to energy metabolism pathways, as compared to 17 in DCM and 3 in IC. Significantly, 6 beta-oxidation enzymes were reduced in CCC, while only 2 of them were down-regulated in DCM and 1 in IC. We also observed that the cytokine IFN-gamma, previously described with increased levels in CCC, reduces mitochondrial membrane potential in cardiomyocytes. Results suggest a major reduction of mitochondrial energy metabolism and mitochondrial dysfunction in CCC myocardium which may be in part linked to IFN-gamma. This may partially explain the worse prognosis of CCC as compared to DCM or IC.
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Affiliation(s)
- Priscila Camillo Teixeira
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Axel Ducret
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Hanno Langen
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Everson Nogoceke
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | | | - João Paulo Silva Nunes
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,INSERM, UMR_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France.,Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia, INCT, iii- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Luiz Benvenuti
- Anatomical Pathology Division, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Debora Levy
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sergio Paulo Bydlowski
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Edimar Alcides Bocchi
- Heart Failure Team, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Andréia Kuramoto Takara
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alfredo Inácio Fiorelli
- Division of Surgery, Heart Institute, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Noedir Antonio Stolf
- Division of Surgery, Heart Institute, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Pablo Pomeranzeff
- Division of Surgery, Heart Institute, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Christophe Chevillard
- INSERM, UMR_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Jorge Kalil
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia, INCT, iii- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute (Incor) Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Division of Clinical Immunology and Allergy, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia, INCT, iii- Institute for Investigation in Immunology, São Paulo, Brazil
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8
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Zhang B, Li X, Liu G, Zhang C, Zhang X, Shen Q, Sun G, Sun X. Peroxiredomin-4 ameliorates lipotoxicity-induced oxidative stress and apoptosis in diabetic cardiomyopathy. Biomed Pharmacother 2021; 141:111780. [PMID: 34130124 DOI: 10.1016/j.biopha.2021.111780] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/11/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Diabetic cardiomyopathy (DCM), one severe complication in the diabetes, leads to high mortality in the diabetic patients. However, the understanding of molecular mechanisms underlying DCM is far from completion. Herein, we investigated the disease-related differences in the proteomes of DCM based on db/db mice and verified the protective roles of peroxiredoxin-4 (Prdx4) in H9c2 cardiomyocytes treated by palmitic acid (PA). Fasting blood glucose (FBG) and cardiac function was detected in the 6-month-old control and diabetic mice. The hearts were then collected and analyzed by a coupled label-free and mass spectrometry approach. In vivo investigation indicated that body weight and FBG of db/db mice markedly increased, and diabetic heart exhibited obvious cardiac hypertrophy and lipid droplet accumulation, and cardiac dysfunction as is indicated by the increases of left ventricle posterior wall thickness in systole (LVPWd) and diastole (LVPWs), and reduction of fractional shortening (FS). We used proteomic analysis and then detected a grand total of 2636 proteins. 175 differentially expressed proteins (DEPs) were markedly detected in the diabetic heart. Thereinto, Prdx4 was markedly down-regulated in the diabetic heart. In vitro experiments revealed that 250 μM PA significantly inhibited viability of H9c2 cell. PA induced much accumulation of lipid droplet in cardiomyocytes and resulted in an increase of mRNA expressions of lipogenic genes (FASN and SCD1) and cardiac hypertrophic genes. Additionally, protein level of Prdx4 evidently reduced in the PA-treated H9c2 cell. It was further found that shRNA-mediated Prdx4 knockdown exacerbated PA-induced oxidative stress and cardiomyocyte apoptosis, whereas overexpressing Prdx4 in the H9c2 cells noteworthily limited PA-induced ROS generation and cardiomyocytes apoptosis. These data collectively reveal the essential role of abnormal Prdx4 in pathological alteration of DCM, and provide potentially therapeutic target for the prevention of DCM.
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Affiliation(s)
- Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Xiaoya Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Guoxin Liu
- Department of Pharmacy, The Third People's Hospital of Qingdao, Qingdao 266071, Shandong, China.
| | - Chenyang Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Xuelian Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Qiang Shen
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Guibo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China.
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9
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Li S, Hu L, Zhang C. Urinary vitamin D-binding protein as a marker of ovarian reserve. Reprod Biol Endocrinol 2021; 19:80. [PMID: 34074317 PMCID: PMC8168315 DOI: 10.1186/s12958-021-00762-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Ovarian reserve reflects the quality and quantity of available oocytes and has become an indispensable measure for the better understanding of reproductive potential. Proteomic approaches are especially helpful in discerning differential protein expression patterns associated with normal and diseased states and, thus, proteomic analyses are increasingly used to identify clinically useful biomarkers. The aim of this study was to investigate proteins secreted in the urine of patients with different ovarian reserve by proteomic techniques to identify potential markers for assessing ovarian reserve. METHODS Urine samples were obtained from patients with polycystic ovary syndrome (PCOS) and diminished ovarian reserve (DOR), and from normal control (NC)participants. We used isobaric tags for relative and absolute quantification (iTRAQ) technology combined with mass spectrometry analysis to identify candidate urinary proteins in the three groups. The selected proteins were confirmed using western blot analysis and enzyme-linked immunosorbent assay (ELISA). Diagnostic performance of the selected proteins was assessed using receiver operating characteristic analysis. RESULTS When Compared with NC samples, 285 differentially expressed proteins (DEPs) were identified in the DOR samples and 372 in the PCOS samples. By analyzing the intersection of the two groups of DEPs, we found 26 proteins with different expression trends in the DOR and PCOS groups. Vitamin D-binding protein (VDBP) was the key protein for the protein-protein interaction network. ELISA quantification of urinary VDBP revealed the highest levels in the PCOS group, followed by the NC group and the lowest levels in the DOR group (115.90 ± 26.02, 81.86 ± 23.92 and 52.84 ± 21.37 ng/ml, respectively; P < 0.05). As a diagnostic marker, VDBP had a sensitivity of 67.4% and a specificity of 91.8% for DOR, and a sensitivity of 93.8% and a specificity of 77.6% for PCOS. CONCLUSIONS Urinary VDBP is closely associated with ovarian reserve and can be considered as a novel noninvasive biomarker of ovarian reserve. However, studies including large sample sizes are needed to validate these results.
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Affiliation(s)
- Sanglin Li
- Reproductive Medicine Center, Department of Gynecology and Obstetrics, The Second Affiliated Hospital, Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010, China.
| | - Lina Hu
- Reproductive Medicine Center, Department of Gynecology and Obstetrics, The Second Affiliated Hospital, Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010, China
| | - Chanyu Zhang
- Reproductive Medicine Center, Department of Gynecology and Obstetrics, The Second Affiliated Hospital, Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010, China
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10
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Fernandes Vileigas D, Cicogna AC. Effects of obesity on the cardiac proteome. ENDOCRINE AND METABOLIC SCIENCE 2021. [DOI: 10.1016/j.endmts.2020.100076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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11
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Zhang S, Wu P, Liu J, Du Y, Yang Z. Roflumilast Attenuates Doxorubicin-Induced Cardiotoxicity by Targeting Inflammation and Cellular Senescence in Cardiomyocytes Mediated by SIRT1. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:87-97. [PMID: 33469262 PMCID: PMC7810683 DOI: 10.2147/dddt.s269029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022]
Abstract
Background and Purpose Cardiotoxicity is an important side effect of the treatment of a malignant tumor with Doxorubicin. Currently, decreasing the dosage of Doxorubicin to alleviate the side effects on cardiac function is the common method to deal with the cardiotoxicity induced by Doxorubicin. The present study aims to investigate the therapeutic effects of Roflumilast on Doxorubicin-induced inflammation and cellular senescence, as well as the potential mechanism in H9c2 myocardial cells. Methods The injured cardiac cell model was established by incubation with 5 μmol/L Doxorubicin. MTT was used to evaluate the cell viability of treated H9c2 cardiac cells. The expression of 4-HNE was determined using an immunofluorescence assay. The gene expression levels of IL-17, IL-6, TNF-α, IL-4, PAI-1, p21, and SIRT1 were evaluated using qRT-PCR and the protein levels of Gpx4, PAI-1, p21, and SIRT1 were determined using Western blot analysis. Secretions of IL-17, IL-6, TNF-α, IL-4, CK-MB, and cTnI were measured using ELISA. Cellular senescence was assessed using SA-β-Gal staining. Si-RNA technology was used to knockdown the expression of SIRT1 in H9c2 cardiac cells. Results Cell viability of H9c2 cardiac cells was significantly inhibited by Doxorubicin but rescued by Roflumilast. The upregulated 4-HNE and downregulated Gpx4 were reversed by Roflumilast. The secretions of IL-6 and IL-17 were promoted by Doxorubicin and suppressed by Roflumilast. The increased SA-β-Gal staining induced by Doxorubicin was inhibited by Roflumilast. P21 and PAI-1 were significantly upregulated and SIRT1 was greatly downregulated by Doxorubicin, all of which were reversed by Roflumilast. The anti-senescent effect of Roflumilast was abolished by knocking down SIRT1. Conclusion Roflumilast might attenuate Doxorubicin-induced inflammation and cellular senescence in cardiomyocytes by upregulating SIRT1.
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Affiliation(s)
- Sheng Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China.,Department of Cardiology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu 213004, People's Republic of China
| | - Peng Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Jiabao Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Yingqiang Du
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Zhijian Yang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
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12
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Vileigas DF, Harman VM, Freire PP, Marciano CLC, Sant'Ana PG, de Souza SLB, Mota GAF, da Silva VL, Campos DHS, Padovani CR, Okoshi K, Beynon RJ, Santos LD, Cicogna AC. Landscape of heart proteome changes in a diet-induced obesity model. Sci Rep 2019; 9:18050. [PMID: 31792287 PMCID: PMC6888820 DOI: 10.1038/s41598-019-54522-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
Obesity is a pandemic associated with a high incidence of cardiovascular disease; however, the mechanisms are not fully elucidated. Proteomics may provide a more in-depth understanding of the pathophysiological mechanisms and contribute to the identification of potential therapeutic targets. Thus, our study evaluated myocardial protein expression in healthy and obese rats, employing two proteomic approaches. Male Wistar rats were established in two groups (n = 13/group): control diet and Western diet fed for 41 weeks. Obesity was determined by the adipose index, and cardiac function was evaluated in vivo by echocardiogram and in vitro by isolated papillary muscle analysis. Proteomics was based on two-dimensional gel electrophoresis (2-DE) along with mass spectrometry identification, and shotgun proteomics with label-free quantification. The Western diet was efficient in triggering obesity and impaired contractile function in vitro; however, no cardiac dysfunction was observed in vivo. The combination of two proteomic approaches was able to increase the cardiac proteomic map and to identify 82 differentially expressed proteins involved in different biological processes, mainly metabolism. Furthermore, the data also indicated a cardiac alteration in fatty acids transport, antioxidant defence, cytoskeleton, and proteasome complex, which have not previously been associated with obesity. Thus, we define a robust alteration in the myocardial proteome of diet-induced obese rats, even before functional impairment could be detected in vivo by echocardiogram.
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Affiliation(s)
- Danielle F Vileigas
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil.
| | - Victoria M Harman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, L69 7ZB, United Kingdom
| | - Paula P Freire
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618970, Brazil
| | - Cecília L C Marciano
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Paula G Sant'Ana
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Sérgio L B de Souza
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Gustavo A F Mota
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Vitor L da Silva
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Dijon H S Campos
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Carlos R Padovani
- Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618970, Brazil
| | - Katashi Okoshi
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, L69 7ZB, United Kingdom
| | - Lucilene D Santos
- Center for the Study of Venoms and Venomous Animals (CEVAP)/Graduate Program in Tropical Diseases (FMB), São Paulo State University (UNESP), Botucatu, São Paulo, 18610307, Brazil
| | - Antonio C Cicogna
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, 18618687, Brazil.
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13
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Coats CJ, Heywood WE, Virasami A, Ashrafi N, Syrris P, Dos Remedios C, Treibel TA, Moon JC, Lopes LR, McGregor CGA, Ashworth M, Sebire NJ, McKenna WJ, Mills K, Elliott PM. Proteomic Analysis of the Myocardium in Hypertrophic Obstructive Cardiomyopathy. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e001974. [PMID: 30562113 DOI: 10.1161/circgen.117.001974] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is characterized by a complex phenotype that is only partly explained by the biological effects of individual genetic variants. The aim of this study was to use proteomic analysis of myocardial tissue to explore the postgenomic phenotype. METHODS Label-free proteomic analysis was used initially to compare protein profiles in myocardial samples from 11 patients with HCM undergoing surgical myectomy with control samples from 6 healthy unused donor hearts. Differentially expressed proteins of interest were validated in myocardial samples from 65 unrelated individuals (HCM [n=51], controls [n=7], and aortic stenosis [n=7]) by the development and use of targeted multiple reaction monitoring-based triple quadrupole mass spectrometry. RESULTS In this exploratory study, 1586 proteins were identified with 151 proteins differentially expressed in HCM samples compared with controls ( P<0.05). Protein expression profiling showed that many proteins identified in the initial discovery study were associated with metabolism, muscle contraction, calcium regulation, and oxidative stress. Proteins downregulated in HCM versus controls included creatine kinase M-type, fructose-bisphosphate aldolase A, and phosphoglycerate mutase ( P<0.001). Proteins upregulated in HCM included lumican, carbonic anhydrase 3, desmin, α-actin skeletal, and FHL1 (four and a half LIM domain protein 1; P<0.01). Myocardial lumican concentration correlated with the left atrial area (ρ=0.34, P=0.015), late gadolinium enhancement on cardiac magnetic resonance imaging ( P=0.03) and the presence of a pathogenic sarcomere mutation ( P=0.04). CONCLUSIONS The myocardial proteome of HCM provides supporting evidence for dysregulation of metabolic and structural proteins. The finding that lumican is raised in HCM hearts provides insight into the myocardial fibrosis that characterizes this disease.
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Affiliation(s)
- Caroline J Coats
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.).,University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Wendy E Heywood
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Alex Virasami
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - Nadia Ashrafi
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Petros Syrris
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Cris Dos Remedios
- Department of Anatomy and Histology, Bosch Institute, The University of Sydney, New South Wales, Australia (C.d.R.)
| | - Thomas A Treibel
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.).,Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - James C Moon
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.).,Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - Luis R Lopes
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.).,Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - Christopher G A McGregor
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Michael Ashworth
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - Neil J Sebire
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - William J McKenna
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Kevin Mills
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Perry M Elliott
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.).,Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
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14
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Coats CJ, Heywood WE, Virasami A, Ashrafi N, Syrris P, dos Remedios C, Treibel TA, Moon JC, Lopes LR, McGregor CG, Ashworth M, Sebire NJ, McKenna WJ, Mills K, Elliott PM. Proteomic Analysis of the Myocardium in Hypertrophic Obstructive Cardiomyopathy. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2018. [DOI: 10.1161/circgenetics.117.001974] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Caroline J. Coats
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Wendy E. Heywood
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Alex Virasami
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - Nadia Ashrafi
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Petros Syrris
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Cris dos Remedios
- Department of Anatomy and Histology, Bosch Institute, The University of Sydney, New South Wales, Australia (C.d.R.)
| | - Thomas A. Treibel
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
- Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - James C. Moon
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
- Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - Luis R. Lopes
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
- Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
| | - Christopher G.A. McGregor
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Michael Ashworth
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - Neil J. Sebire
- Histopathology Unit, Great Ormond Street Hospital for Children, London, United Kingdom (A.V., M.A., N.J.S.)
| | - William J. McKenna
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
| | - Kevin Mills
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom (C.J.C., W.E.H., N.A., K.M.)
| | - Perry M. Elliott
- University College London Institute of Cardiovascular Science, London, United Kingdom (C.J.C., P.S., T.A.T., J.C.M., L.R.L., C.G.A.M., W.J.M., P.M.E.)
- Barts Heart Centre, Barts Health NHS Trust, London, United Kingdom (T.A.T., J.C.M., L.R.L., P.M.E.)
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15
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Eckhardt A, Kulhava L, Miksik I, Pataridis S, Hlavackova M, Vasinova J, Kolar F, Sedmera D, Ostadal B. Proteomic analysis of cardiac ventricles: baso-apical differences. Mol Cell Biochem 2018; 445:211-219. [PMID: 29302836 DOI: 10.1007/s11010-017-3266-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/23/2017] [Indexed: 12/19/2022]
Abstract
The heart is characterized by a remarkable degree of heterogeneity. Since different cardiac pathologies affect different cardiac regions, it is important to understand molecular mechanisms by which these parts respond to pathological stimuli. In addition to already described left ventricular (LV)/right ventricular (RV) and transmural differences, possible baso-apical heterogeneity has to be taken into consideration. The aim of our study has been, therefore, to compare proteomes in the apical and basal parts of the rat RV and LV. Two-dimensional electrophoresis was used for the proteomic analysis. The major result of this study has revealed for the first time significant baso-apical differences in concentration of several proteins, both in the LV and RV. As far as the LV is concerned, five proteins had higher concentration in the apical compared to basal part of the ventricle. Three of them are mitochondrial and belong to the "metabolism and energy pathways" (myofibrillar creatine kinase M-type, L-lactate dehydrogenase, dihydrolipoamide dehydrogenase). Myosin light chain 3 is a contractile protein and HSP60 belongs to heat shock proteins. In the RV, higher concentration in the apical part was observed in two mitochondrial proteins (creatine kinase S-type and proton pumping NADH:ubiquinone oxidoreductase). The described changes were more pronounced in the LV, which is subjected to higher workload. However, in both chambers was the concentration of proteins markedly higher in the apical than that in basal part, which corresponds to the higher energetic demand and contractile activity of these segments of both ventricles.
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Affiliation(s)
- Adam Eckhardt
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.
| | - Lucie Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague, Czech Republic
| | - Ivan Miksik
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Statis Pataridis
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Marketa Hlavackova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Physiology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Jana Vasinova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Frantisek Kolar
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - David Sedmera
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Kateřinská 32, Prague, Czech Republic
| | - Bohuslav Ostadal
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
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16
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Ichihara S, Suzuki Y, Chang J, Kuzuya K, Inoue C, Kitamura Y, Oikawa S. Involvement of oxidative modification of proteins related to ATP synthesis in the left ventricles of hamsters with cardiomyopathy. Sci Rep 2017; 7:9243. [PMID: 28835655 PMCID: PMC5569096 DOI: 10.1038/s41598-017-08546-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 07/14/2017] [Indexed: 12/21/2022] Open
Abstract
Inflammation enhanced by accumulation of reactive oxygen species plays an essential role in the progression of cardiovascular diseases. Using the 2D-oxyblot analysis and 2D-difference image gel electrophoresis (2D-DIGE), we compared the levels of ROS-induced carbonyl modification of myocardial proteins in the whole left ventricles between 6-week-old hamsters with dilated (TO-2) and hypertrophic cardiomyopathy (Bio14.6) and control hamsters (F1B). Then, 2D electrophoresis combined with MALDI-TOF/TOF tandem mass spectrometry detected 18 proteins with increased carbonyl level in cardiomyopathy hamsters compared with control hamster. Carbonyl modification of proteins related to ATP synthesis, including citric acid cycle and electron transport system, was observed in the hearts of hamsters with both types of cardiomyopathy. Further analysis indicated that left ventricular carbonyl production correlated negatively with succinyl-CoA:3-ketoacid-coenzyme A transferase 1 activity (r 2 = 0.60, P = 0.0007) and ATP concentration (r 2 = 0.29, P = 0.037), suggesting that protein carbonylation has negative effects on the levels of these biomolecules. Furthermore, carbonyl production significantly correlated with plasma Troponin T level (r 2 = 0.33, P = 0.026). Reduction of energy metabolism by oxidative damage may contribute to the development of left ventricular impairment in cardiomyopathy.
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Affiliation(s)
- Sahoko Ichihara
- Graduate School of Regional Innovation Studies, Tsu, Japan.
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan.
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan.
| | - Yuka Suzuki
- Graduate School of Regional Innovation Studies, Tsu, Japan
- Community-University Research Cooperation Center, Mie University, Tsu, Japan
| | - Jie Chang
- Graduate School of Regional Innovation Studies, Tsu, Japan
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Kentaro Kuzuya
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan
| | - Chisa Inoue
- Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Japan
| | - Yuki Kitamura
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Tsu, Japan
| | - Shinji Oikawa
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Tsu, Japan
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17
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Impact and influence of “omics” technology on hyper tension studies. Int J Cardiol 2017; 228:1022-1034. [DOI: 10.1016/j.ijcard.2016.11.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/06/2016] [Indexed: 12/14/2022]
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18
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Dhingra R, Vasan RS. Biomarkers in cardiovascular disease: Statistical assessment and section on key novel heart failure biomarkers. Trends Cardiovasc Med 2017; 27:123-133. [PMID: 27576060 PMCID: PMC5253084 DOI: 10.1016/j.tcm.2016.07.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/23/2016] [Accepted: 07/23/2016] [Indexed: 12/11/2022]
Abstract
Cardiovascular disease (CVD) is a leading cause of death worldwide and continues to increase in prevalence compared to previous decades, in part because of the aging of the world population. Atherosclerotic CVD starts at a very young age and progresses over time allowing sufficient time for screening and early detection of the condition. Advances in biomarker research and developments related to CVD over the past 30 years have led to more sensitive screening methods, a greater emphasis on its early detection and diagnosis, and improved treatments resulting in more favorable clinical outcomes in the community. However, the use of biomarkers for different purposes in CVD remains an important area of research that has been explored by scientists over the years and many new developments are still underway. Therefore, a detailed description of all CVD biomarkers that are currently been used or investigated for future use in the field of cardiovascular medicine is out of scope for any review article. In the present review, we do not intend to replicate the information from previous exhaustive review on biomarkers, but highlight key statistical and clinical issues with an emphasis on methods to evaluate the incremental yield of biomarkers, including their clinical utility, a prerequisite before any putative novel biomarker is utilized in clinical practice. In addition, we will summarize information regarding recent novel heart failure biomarkers in current practice, which are undergoing scrutiny before they can be available for clinical use, and their impact on clinical outcomes.
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Affiliation(s)
- Ravi Dhingra
- Division of Cardiovascular Medicine, University of Wisconsin-Madison, 600 Highland Avenue, E5/582C, MC 5710, Madison, WI 53792.
| | - Ramachandran S Vasan
- Division of Cardiovascular Medicine, University of Wisconsin-Madison, 600 Highland Avenue, E5/582C, MC 5710, Madison, WI 53792
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19
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Tan NJ, Daim LDJ, Jamil AAM, Mohtarrudin N, Thilakavathy K. An effective placental cotyledons proteins extraction method for 2D gel electrophoresis. Electrophoresis 2016; 38:633-644. [PMID: 27992069 DOI: 10.1002/elps.201600377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 11/06/2022]
Abstract
Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen.
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Affiliation(s)
- Niu J Tan
- Medical Genetics Unit, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Leona D J Daim
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, Selangor, Malaysia
| | - Amilia A M Jamil
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Norhafizah Mohtarrudin
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Karuppiah Thilakavathy
- Medical Genetics Unit, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
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20
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Lam MPY, Lau E, Ng DCM, Wang D, Ping P. Cardiovascular proteomics in the era of big data: experimental and computational advances. Clin Proteomics 2016; 13:23. [PMID: 27980500 PMCID: PMC5137214 DOI: 10.1186/s12014-016-9124-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/24/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond merely inventorying protein species, and address sophisticated questions on cardiac physiology. The advent of massive mass spectrometry datasets has in turn led to increasing intersection between proteomics and big data science. Here we review new frontiers in technological developments and their applications to cardiovascular medicine. The impact of big data science on cardiovascular proteomics investigations and translation to medicine is highlighted.
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Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Edward Lau
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Dominic C M Ng
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Ding Wang
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
| | - Peipei Ping
- NIH BD2K Center of Excellence at UCLA; Department of Physiology, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Medicine, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA ; Department of Bioinformatics, University of California at Los Angeles, 675 Charles E. Young Drive, Los Angeles, CA 90095 USA
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21
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Santana ET, Feliciano RDS, Serra AJ, Brigidio E, Antonio EL, Tucci PJF, Nathanson L, Morris M, Silva JA. Comparative mRNA and MicroRNA Profiling during Acute Myocardial Infarction Induced by Coronary Occlusion and Ablation Radio-Frequency Currents. Front Physiol 2016; 7:565. [PMID: 27932994 PMCID: PMC5123550 DOI: 10.3389/fphys.2016.00565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
The ligation of the left anterior descending coronary artery is the most commonly used experimental model to induce myocardial infarction (MI) in rodents. A high mortality in the acute phase and the heterogeneity of the size of the MI obtained are drawbacks recognized in this model. In an attempt to solve the problem, our group recently developed a new MI experimental model which is based on application of myocardial ablation radio-frequency currents (AB-RF) that yielded MI with homogeneous sizes and significantly reduce acute mortality. In addition, cardiac structural, and functional changes aroused by AB-RF were similar to those seen in animals with MI induced by coronary artery ligation. Herein, we compared mRNA expression of genes that govern post-MI milieu in occlusion and ablation models. We analyzed 48 mRNAs expressions of nine different signal transduction pathways (cell survival and metabolism signs, matrix extracellular, cell cycle, oxidative stress, apoptosis, calcium signaling, hypertrophy markers, angiogenesis, and inflammation) in rat left ventricle 1 week after MI generated by both coronary occlusion and AB-RF. Furthermore, high-throughput miRNA analysis was also assessed in both MI procedures. Interestingly, mRNA expression levels and miRNA expressions showed strong similarities between both models after MI, with few specificities in each model, activating similar signal transduction pathways. To our knowledge, this is the first comparison of genomic alterations of mRNA and miRNA contents after two different MI procedures and identifies key signaling regulators modulating the pathophysiology of these two models that might culminate in heart failure. Furthermore, these analyses may contribute with the current knowledge concerning transcriptional and post-transcriptional changes of AB-RF protocol, arising as an alternative and effective MI method that reproduces most changes seem in coronary occlusion.
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Affiliation(s)
- Eduardo T Santana
- Rehabilitation Department, Universidade Nove de Julho São Paulo, Brazil
| | - Regiane Dos Santos Feliciano
- Biophotonics Department, Universidade Nove de JulhoSão Paulo, Brazil; Medicine Department, Universidade Nove de JulhoSão Paulo, Brazil
| | - Andrey J Serra
- Biophotonics Department, Universidade Nove de Julho São Paulo, Brazil
| | - Eduardo Brigidio
- Medicine Department, Universidade Nove de Julho São Paulo, Brazil
| | - Ednei L Antonio
- Cardiac Physiology Department, Universidade Federal de São Paulo São Paulo, Brazil
| | - Paulo J F Tucci
- Cardiac Physiology Department, Universidade Federal de São Paulo São Paulo, Brazil
| | - Lubov Nathanson
- Institute for Neuro-Immune Medicine, Nova Southeastern University Fort Lauderdale, FL, USA
| | - Mariana Morris
- Institute for Neuro-Immune Medicine, Nova Southeastern University Fort Lauderdale, FL, USA
| | - José A Silva
- Medicine Department, Universidade Nove de Julho São Paulo, Brazil
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22
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Abstract
Advances in mass spectrometry technology and bioinformatics using clinical human samples have expanded quantitative proteomics in cardiovascular research. There are two major proteomic strategies: namely, "gel-based" or "gel-free" proteomics coupled with either "top-down" or "bottom-up" mass spectrometry. Both are introduced into the proteomic analysis using plasma or serum sample targeting 'biomarker" searches of aortic aneurysm and tissue samples, such as from the aneurysmal wall, calcific aortic valve, or myocardial tissue, investigating pathophysiological protein interactions and post-translational modifications. We summarize the proteomic studies that analyzed human samples taken during cardiovascular surgery to investigate disease processes, in order to better understand the system-wide changes behind known molecular factors and specific signaling pathways.
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Affiliation(s)
- Teiji Oda
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Ken-ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Izumo, Shimane, Japan
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23
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Karimpour-Fard A, Epperson LE, Hunter LE. A survey of computational tools for downstream analysis of proteomic and other omic datasets. Hum Genomics 2015; 9:28. [PMID: 26510531 PMCID: PMC4624643 DOI: 10.1186/s40246-015-0050-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/06/2015] [Indexed: 12/19/2022] Open
Abstract
Proteomics is an expanding area of research into biological systems with significance for biomedical and therapeutic applications ranging from understanding the molecular basis of diseases to testing new treatments, studying the toxicity of drugs, or biotechnological improvements in agriculture. Progress in proteomic technologies and growing interest has resulted in rapid accumulation of proteomic data, and consequently, a great number of tools have become available. In this paper, we review the well-known and ready-to-use tools for classification, clustering and validation, interpretation, and generation of biological information from experimental data. We suggest some rules of thumb for the reader on choosing the best suitable learning method for a particular dataset and conclude with pathway and functional analysis and then provide information about submitting final results to a repository.
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Affiliation(s)
- Anis Karimpour-Fard
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - L Elaine Epperson
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Lawrence E Hunter
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
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24
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Su YR, Chiusa M, Brittain E, Hemnes AR, Absi TS, Lim CC, Di Salvo TG. Right ventricular protein expression profile in end-stage heart failure. Pulm Circ 2015; 5:481-97. [PMID: 26401249 DOI: 10.1086/682219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/30/2014] [Indexed: 11/03/2022] Open
Abstract
Little is known about the right ventricular (RV) proteome in human heart failure (HF), including possible differences compared to the left ventricular (LV) proteome. We used 2-dimensional differential in-gel electrophoresis (pH: 4-7, 10-150 kDa), followed by liquid chromatography tandem mass spectrometry, to compare the RV and LV proteomes in 12 explanted human hearts. We used Western blotting and multiple-reaction monitoring for protein verification and RNA sequencing for messenger RNA and protein expression correlation. In all 12 hearts, the right ventricles (RVs) demonstrated differential expression of 11 proteins relative to the left ventricles (LVs), including lesser expression of CRYM, TPM1, CLU, TXNL1, and COQ9 and greater expression of TNNI3, SAAI, ERP29, ACTN2, HSPB2, and NDUFS3. Principal-components analysis did not suggest RV-versus-LV proteome partitioning. In the nonischemic RVs (n = 6), 7 proteins were differentially expressed relative to the ischemic RVs (n = 6), including increased expression of CRYM, B7Z964, desmin, ANXA5, and MIME and decreased expression of SERPINA1 and ANT3. Principal-components analysis demonstrated partitioning of the nonischemic and ischemic RV proteomes, and gene ontology analysis identified differences in hemostasis and atherosclerosis-associated networks. There were no proteomic differences between RVs with echocardiographic dysfunction (n = 8) and those with normal function (n = 4). Messenger RNA and protein expression did not correlate consistently, suggesting a major role for RV posttranscriptional protein expression regulation. Differences in contractile, cytoskeletal, metabolic, signaling, and survival pathways exist between the RV and the LV in HF and may be related to the underlying HF etiology and differential posttranscriptional regulation.
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Affiliation(s)
- Yan Ru Su
- Division of Cardiovascular Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Manuel Chiusa
- Division of Cardiovascular Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Evan Brittain
- Division of Cardiovascular Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Anna R Hemnes
- Division of Pulmonary Medicine and Critical Care, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Tarek S Absi
- Department of Surgical Science, Division of Cardiac Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Chee Chew Lim
- Division of Cardiovascular Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Thomas G Di Salvo
- Division of Cardiovascular Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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25
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Wende AR. Post-translational modifications of the cardiac proteome in diabetes and heart failure. Proteomics Clin Appl 2015; 10:25-38. [PMID: 26140508 PMCID: PMC4698356 DOI: 10.1002/prca.201500052] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/03/2015] [Accepted: 06/29/2015] [Indexed: 12/19/2022]
Abstract
Cardiovascular complications are the leading cause of death in diabetic patients. Decades of research has focused on altered gene expression, altered cellular signaling, and altered metabolism. This work has led to better understanding of disease progression and treatments aimed at reversing or stopping this deadly process. However, one of the pieces needed to complete the puzzle and bridge the gap between altered gene expression and changes in signaling/metabolism is the proteome and its host of modifications. Defining the mechanisms of regulation includes examining protein levels, localization, and activity of the functional component of cellular machinery. Excess or misutilization of nutrients in obesity and diabetes may lead to PTMs contributing to cardiovascular disease progression. PTMs link regulation of metabolic changes in the healthy and diseased heart with regulation of gene expression itself (e.g. epigenetics), protein enzymatic activity (e.g. mitochondrial oxidative capacity), and function (e.g. contractile machinery). Although a number of PTMs are involved in each of these pathways, we will highlight the role of the serine and threonine O‐linked addition of β‐N‐acetyl‐glucosamine or O‐GlcNAcylation. This nexus of nutrient supply, utilization, and storage allows for the modification and translation of mitochondrial function to many other aspects of the cell.
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Affiliation(s)
- Adam R Wende
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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26
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Fu G, Hu M, Chu L, Zhang M. The Difference Quantity of Urinary Peptides between Two Groups of Type 2 Diabetic Patients with or without Coronary Artery Disease. Int J Endocrinol 2015; 2015:758402. [PMID: 26089891 PMCID: PMC4451558 DOI: 10.1155/2015/758402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/10/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023] Open
Abstract
Objectives. We aim to explore urinary biomarkers that could monitor CAD in type 2 diabetic patients. Materials and Methods. Urine samples from two groups, twenty-eight type 2 diabetic patients with coexisting CAD and thirty type 2 diabetic patients without CAD, were purified by MB-WCX and then analyzed by MALDI-TOF-MS. Subsequently, we compared the urinary peptide signatures of the two groups by use of ClinProTools2.1 and evaluated the potential ability of the differently expressed peptides to distinguish type 2 diabetic patients with coexisting CAD from type 2 diabetic patients without CAD by ROC analysis. Finally, the differently expressed peptides were identified by nanoliquid chromatography-tandem mass spectrometry. Results. There were six differently expressed peptides (m/z 1305.2, 1743.9, 2184.9, 2756.1, 3223.2, and 6196.1) between the two groups of subjects, and they were identified as fragments of isoform 1 of fibrinogen alpha chain precursor, prothrombin precursor, and interalpha-trypsin inhibitor heavy chain H4. The diagnostic efficacy of m/z 2756.1 and m/z 3223.2 was better than the other peptides. Area under ROC of the m/z 2756.1, and m/z 3223.2 was 0.98 and 0.93, respectively. Conclusions. These urinary peptides are potential urinary biomarkers for monitoring of type 2 diabetic patients with CAD.
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Affiliation(s)
- Guangzhen Fu
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
| | - Mei Hu
- Department of Clinical Laboratory, Capital Medical University, Beijing Shijitan Hospital, Beijing 100038, China
| | - Lina Chu
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
| | - Man Zhang
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
- Department of Clinical Laboratory, Capital Medical University, Beijing Shijitan Hospital, Beijing 100038, China
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27
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Hsieh SR, Cheng WC, Su YM, Chiu CH, Liou YM. Molecular targets for anti-oxidative protection of green tea polyphenols against myocardial ischemic injury. Biomedicine (Taipei) 2014; 4:23. [PMID: 25520936 PMCID: PMC4264984 DOI: 10.7603/s40681-014-0023-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/14/2014] [Indexed: 12/20/2022] Open
Abstract
Ischemic heart disease is the leading cause of death worldwide. An improved understanding of the mechanisms involved in myocardial injury would allow intervention downstream in the pathway where certain drugs including natural products could be efficiently applied to target the end effectors of the cell death pathway. Green tea polyphenols (GTPs) have potent anti-oxidative capabilities, which may account for their beneficial effects in preventing oxidative stress associated with ischemia injury. Although studies have provided convincing evidence to support the protective effects of GTPs in cardiovascular system, the potential end effectors that mediate cardiac protection are only beginning to be addressed. Proteomics analyses widely used to identify the protein targets for many cardiovascular diseases have advanced the discovery of the signaling mechanism for GTPs-mediated cardio-protection. This review focuses on putative triggers, mediators, and end effectors for the GTPs-mediated cardio-protection signaling pathways engaged in myocardial ischemia crisis, allowing a promising natural product to be used for ameliorating oxidative stress associated with ischemic heart diseases.
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Affiliation(s)
- Shih-Rong Hsieh
- Department of Cardiovascular Surgery, Taichung Veterans General Hospital, 407 Taichung, Taiwan
| | - Wei-Chen Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 300 Hsinchu, Taiwan
| | - Yi-Min Su
- Department of Life Sciences, National Chung-Hsing University, 402 No. 250, Kuokang Road, Taichung, Taiwan
| | - Chun-Hwei Chiu
- Department of Life Sciences, National Chung-Hsing University, 402 No. 250, Kuokang Road, Taichung, Taiwan
| | - Ying-Ming Liou
- Department of Life Sciences, National Chung-Hsing University, 402 No. 250, Kuokang Road, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, 402 Taichung, Taiwan
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28
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Mitra A, Basak T, Ahmad S, Datta K, Datta R, Sengupta S, Sarkar S. Comparative Proteome Profiling during Cardiac Hypertrophy and Myocardial Infarction Reveals Altered Glucose Oxidation by Differential Activation of Pyruvate Dehydrogenase E1 Component Subunit β. J Mol Biol 2014; 427:2104-20. [PMID: 25451023 DOI: 10.1016/j.jmb.2014.10.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/09/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022]
Abstract
Cardiac hypertrophy and myocardial infarction (MI) are two etiologically different disease forms with varied pathological characteristics. However, the precise molecular mechanisms and specific causal proteins associated with these diseases are obscure to date. In this study, a comparative cardiac proteome profiling was performed in Wistar rat models for diseased and control (sham) groups using two-dimensional difference gel electrophoresis followed by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. Proteins were identified using Protein Pilot™ software (version 4.0) and were subjected to stringent statistical analysis. Alteration of key proteins was validated by Western blot analysis. The differentially expressed protein sets identified in this study were associated with different functional groups, involving various metabolic pathways, stress responses, cytoskeletal organization, apoptotic signaling and other miscellaneous functions. It was further deciphered that altered energy metabolism during hypertrophy in comparison to MI may be predominantly attributed to induced glucose oxidation level, via reduced phosphorylation of pyruvate dehydrogenase E1 component subunit β (PDHE1-B) protein during hypertrophy. This study reports for the first time the global changes in rat cardiac proteome during two etiologically different cardiac diseases and identifies key signaling regulators modulating ontogeny of these two diseases culminating in heart failure. This study also pointed toward differential activation of PDHE1-B that accounts for upregulation of glucose oxidation during hypertrophy. Downstream analysis of altered proteome and the associated modulators would enhance our present knowledge regarding altered pathophysiology of these two etiologically different cardiac disease forms.
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Affiliation(s)
- Arkadeep Mitra
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Shadab Ahmad
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Kaberi Datta
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Ritwik Datta
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Sagartirtha Sarkar
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India.
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29
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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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30
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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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31
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Proteomic profiling of the dystrophin-deficient mdx phenocopy of dystrophinopathy-associated cardiomyopathy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:246195. [PMID: 24772416 PMCID: PMC3977469 DOI: 10.1155/2014/246195] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/16/2014] [Indexed: 01/07/2023]
Abstract
Cardiorespiratory complications are frequent symptoms of Duchenne muscular dystrophy, a neuromuscular disorder caused by primary abnormalities in the dystrophin gene. Loss of cardiac dystrophin initially leads to changes in dystrophin-associated glycoproteins and subsequently triggers secondarily sarcolemmal disintegration, fibre necrosis, fibrosis, fatty tissue replacement, and interstitial inflammation. This results in progressive cardiac disease, which is the cause of death in a considerable number of patients afflicted with X-linked muscular dystrophy. In order to better define the molecular pathogenesis of this type of cardiomyopathy, several studies have applied mass spectrometry-based proteomics to determine proteome-wide alterations in dystrophinopathy-associated cardiomyopathy. Proteomic studies included both gel-based and label-free mass spectrometric surveys of dystrophin-deficient heart muscle from the established mdx animal model of dystrophinopathy. Comparative cardiac proteomics revealed novel changes in proteins associated with mitochondrial energy metabolism, glycolysis, signaling, iron binding, antibody response, fibre contraction, basal lamina stabilisation, and cytoskeletal organisation. This review summarizes the importance of studying cardiomyopathy within the field of muscular dystrophy research, outlines key features of the mdx heart and its suitability as a model system for studying cardiac pathogenesis, and discusses the impact of recent proteomic findings for exploring molecular and cellular aspects of cardiac abnormalities in inherited muscular dystrophies.
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Govender P, Baugh JA, Pennington SR, Dunn MJ, Donnelly SC. Role of proteomics in the investigation of pulmonary fibrosis. Expert Rev Proteomics 2014; 4:379-88. [PMID: 17552922 DOI: 10.1586/14789450.4.3.379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pulmonary fibrosis arises as a consequence of aberrant remodeling and defective repair mechanisms within the lung. This destructive process is the cause of much of the morbidity and mortality in many pulmonary disorders. Unfortunately, therapeutic options are limited. A significant advancement in the management of patients with pulmonary fibrosis would be the identification of biomarkers for diagnosis, prognosis and prediction of patient response to therapy. Bronchoalveolar lavage is an ideal tissue target for the discovery of these potential biomarkers in pulmonary fibrosis. Integrative approaches using both gel- and mass spectrometry-based proteomic workflows will allow full coverage of this complex proteome, thereby unlocking this potential information as a clinical tool to aid diagnosis and guide treatment for individual patients with pulmonary fibrosis.
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Affiliation(s)
- Praveen Govender
- University College Dublin, School of Medicine & Medical Science, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
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Qualtieri A, Urso E, Pera ML, Sprovieri T, Bossio S, Gambardella A, Quattrone A. Proteomic profiling of cerebrospinal fluid in Creutzfeldt–Jakob disease. Expert Rev Proteomics 2014; 7:907-17. [DOI: 10.1586/epr.10.80] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zabel C, Andreew A, Mao L, Hartl D. Protein expression overlap: more important than which proteins change in expression? Expert Rev Proteomics 2014; 5:187-205. [DOI: 10.1586/14789450.5.2.187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Li C, Qiu Q, Wang Y, Li P, Xiao C, Wang H, Lin Y, Wang W. Time course label-free quantitative analysis of cardiac muscles of rats after myocardial infarction. MOLECULAR BIOSYSTEMS 2014; 10:505-13. [PMID: 24382414 DOI: 10.1039/c3mb70422j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Heart failure is a worldwide cause of mortality and morbidity and is the ultimate ending of a variety of complex diseases. This reflects our incomplete understanding of its underlying molecular mechanisms and furthermore increases the complexity of the disease. To better understand the molecular mechanisms of heart failure, we investigated dynamic proteomic differences between the heart tissue of myocardial infarction rats and the rats in the sham group at days 4, 14, 28, 45 after operation. Using a label-free quantitative proteomic approach based on nanoscale ultra-performance liquid chromatography-ESI-MS(E), 133 proteins were identified at the four time points in 8 groups. 13 non-redundant proteins changed dynamically after acute myocardial infarction (AMI) in rat left ventricular (LV) tissue, including cytoskeletal proteins, metabolic enzymes, oxidative stress related proteins and ion channel proteins. The network analysis showed that the differential protein might play an important role in lipid metabolism and hypertrophic cardiomyopathy. The dynamic changes in the expression of beta-actin, alpha B-crystallin (CryAB), heat shock protein 8(HSP8), desmin and l-lactate dehydrogenase B (LDHB) were tested by the western-blot assay, and the results were consistent with the label-free quantitative proteomic results. Correlative analysis indicates that the CryAB and desmin have a better linear relation with heart function (ejection fraction) than cardiac troponin T (cTNT). Our results provide the first experimental evidence of the proteins that are differentially expressed following myocardial infarction, using time-course label-free quantitative proteomics in vivo without ischemia-reperfusion injury or myocardial ischemia. These differential functional proteins (especially CryAB and desmin) have different patterns during the myocardial infarction, which may partially account for the underlying mechanisms involved in cardiac rehabilitation.
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Affiliation(s)
- Chun Li
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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36
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Proteomic remodeling of proteasome in right heart failure. J Mol Cell Cardiol 2014; 66:41-52. [DOI: 10.1016/j.yjmcc.2013.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 09/13/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
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Hammer E, Darm K, Völker U. Characterization of the human myocardial proteome in dilated cardiomyopathy by label-free quantitative shotgun proteomics of heart biopsies. Methods Mol Biol 2013; 1005:67-76. [PMID: 23606249 DOI: 10.1007/978-1-62703-386-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteomic profiling of heart tissue might help to discover the molecular events related to or even causing cardiovascular diseases in human. However, this material is rare and only available from biopsies taken for diagnostics, e.g., assessment of inflammatory events or virus persistence. Within this chapter, we describe a workflow for the quantitative proteome analysis of heart biopsies. Starting with 1-2 mg of tissue material, crude protein extracts were prepared, digested with LysC and trypsin, and then analyzed by LC-ESI-tandem mass spectrometry. Due to the low technical variance, the method can be used for label-free quantitation of disease-specific alterations in the human heart. Methods discussed include homogenization of biopsy tissue, sample preparation, proteolytic digestion, as well as data analysis for label-free quantitation.
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Affiliation(s)
- Elke Hammer
- Abteilung für Funktionelle Genomforschung, Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Greifswald, Germany
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Wang Y, Li C, Chuo W, Liu Z, Ouyang Y, Li D, Han J, Wu Y, Guo S, Wang W. Integrated proteomic and metabolomic analysis reveals the NADH-mediated TCA cycle and energy metabolism disorders based on a new model of chronic progressive heart failure. MOLECULAR BIOSYSTEMS 2013; 9:3135-45. [PMID: 24108264 DOI: 10.1039/c3mb70263d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Despite major advances in the treatment of heart failure (HF), it remains the major cause of mortality and morbidity worldwide. Experimental models of HF typically utilize acute myocardial infarction. However, the majority of clinical HFs occur gradually by a chronic progressive mechanism. Thus, more relevant models are required to aid identification, quantification, and characterization of HF, and its underlying mechanisms. METHODS AND FINDINGS We developed a model of progressive chronic heart failure (CHF) in the mini-swine by placement of an ameroid constrictor on the left anterior descending coronary artery (LAD). This model demonstrated a steady decline in the cardiac function from 8 to 12 weeks, with a 50% reduction in the ejection fraction. Further, the proteomic, metabolomic and bioinformatic analyses of ischemic tissue and plasma revealed a significant alteration of the mitochondrial respiratory chain mediated by nicotinamide adenine dinucleotide (NADH), which resulted in down-regulation of malate dehydrogenase (MDH) and insufficient energy supply to support cardiac contractility and relaxation. Furthermore, significant changes in apolipoprotein A-I, low density lipoprotein (LDL), and very LDL (VLDL) in plasma indicated that lipid metabolism disorders occurred in mini-swines with myocardial ischemia via glycerolipid metabolism. CONCLUSIONS We describe a stable and easily reproducible CHF model using an ameroid constrictor placed on the LAD. We found that the NADH-mediated tricarboxylic acid cycle and energy metabolism disorders are key pathophysiological mechanisms underlying CHF. These data will provide potential biomarkers for monitoring the therapeutic intervention of CHF.
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Affiliation(s)
- Yong Wang
- Beijing University of Chinese Medicine, Beijing 100029, China.
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Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N, Chakraborty S. Comparative Proteomics Reveals a Role for Seed Storage Protein AmA1 in Cellular Growth, Development, and Nutrient Accumulation. J Proteome Res 2013; 12:4904-30. [DOI: 10.1021/pr4007987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalit Agrawal
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Kanika Narula
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Swaraj Basu
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Shubhendu Shekhar
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Sudip Ghosh
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Asis Datta
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
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Chakraborty N, Ghosh R, Ghosh S, Narula K, Tayal R, Datta A, Chakraborty S. Reduction of oxalate levels in tomato fruit and consequent metabolic remodeling following overexpression of a fungal oxalate decarboxylase. PLANT PHYSIOLOGY 2013; 162:364-378. [PMID: 23482874 PMCID: PMC3641215 DOI: 10.1104/pp.112.209197] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/09/2013] [Indexed: 05/29/2023]
Abstract
The plant metabolite oxalic acid is increasingly recognized as a food toxin with negative effects on human nutrition. Decarboxylative degradation of oxalic acid is catalyzed, in a substrate-specific reaction, by oxalate decarboxylase (OXDC), forming formic acid and carbon dioxide. Attempts to date to reduce oxalic acid levels and to understand the biological significance of OXDC in crop plants have met with little success. To investigate the role of OXDC and the metabolic consequences of oxalate down-regulation in a heterotrophic, oxalic acid-accumulating fruit, we generated transgenic tomato (Solanum lycopersicum) plants expressing an OXDC (FvOXDC) from the fungus Flammulina velutipes specifically in the fruit. These E8.2-OXDC fruit showed up to a 90% reduction in oxalate content, which correlated with concomitant increases in calcium, iron, and citrate. Expression of OXDC affected neither carbon dioxide assimilation rates nor resulted in any detectable morphological differences in the transgenic plants. Comparative proteomic analysis suggested that metabolic remodeling was associated with the decrease in oxalate content in transgenic fruit. Examination of the E8.2-OXDC fruit proteome revealed that OXDC-responsive proteins involved in metabolism and stress responses represented the most substantially up- and down-regulated categories, respectively, in the transgenic fruit, compared with those of wild-type plants. Collectively, our study provides insights into OXDC-regulated metabolic networks and may provide a widely applicable strategy for enhancing crop nutritional value.
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Drews O. High-resolution separation of cardiovascular proteomes: two-dimensional electrophoresis and liquid chromatography. ACTA ACUST UNITED AC 2013; 5:592. [PMID: 23074339 DOI: 10.1161/circgenetics.110.958637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Oliver Drews
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany.
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Cosme J, Emili A, Gramolini AO. Large-scale characterization of the murine cardiac proteome. Methods Mol Biol 2013; 1005:1-10. [PMID: 23606244 DOI: 10.1007/978-1-62703-386-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cardiomyopathies are diseases of the heart that result in impaired cardiac muscle function. This dysfunction can progress to an inability to supply blood to the body. Cardiovascular diseases play a large role in overall global morbidity. Investigating the protein changes in the heart during disease can uncover pathophysiological mechanisms and potential therapeutic targets. Establishing a global protein expression "footprint" can facilitate more targeted studies of diseases of the heart.In the technical review presented here, we present methods to elucidate the heart's proteome through subfractionation of the cellular compartments to reduce sample complexity and improve detection of lower abundant proteins during multidimensional protein identification technology analysis. Analysis of the cytosolic, microsomal, and mitochondrial subproteomes separately in order to characterize the murine cardiac proteome is advantageous by simplifying complex cardiac protein mixtures. In combination with bioinformatic analysis and genome correlation, large-scale protein changes can be identified at the cellular compartment level in this animal model.
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Affiliation(s)
- Jake Cosme
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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Abstract
The conventional reductionist approach to cardiovascular research investigates individual candidate factors or linear signalling pathways but ignores more complex interactions in biological systems. The advent of molecular profiling technologies that focus on a global characterization of whole complements allows an exploration of the interconnectivity of pathways during pathophysiologically relevant processes, but has brought about the issue of statistical analysis and data integration. Proteins identified by differential expression as well as those in protein–protein interaction networks identified through experiments and through computational modelling techniques can be used as an initial starting point for functional analyses. In combination with other ‘-omics’ technologies, such as transcriptomics and metabolomics, proteomics explores different aspects of disease, and the different pillars of observations facilitate the data integration in disease-specific networks. Ultimately, a systems biology approach may advance our understanding of cardiovascular disease processes at a ‘biological pathway’ instead of a ‘single molecule’ level and accelerate progress towards disease-modifying interventions.
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Affiliation(s)
- Sarah R Langley
- King's British Heart Foundation Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
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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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Fornai L, Angelini A, Klinkert I, Giskes F, Kiss A, Eijkel G, Hove EAAV, Klerk LA, Fedrigo M, Pieraccini G, Moneti G, Valente M, Thiene G, Heeren RMA. Three-dimensional molecular reconstruction of rat heart with mass spectrometry imaging. Anal Bioanal Chem 2012; 404:2927-38. [DOI: 10.1007/s00216-012-6451-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/17/2012] [Accepted: 09/21/2012] [Indexed: 01/03/2023]
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Yuan C, Solaro RJ. Myofilament proteins: From cardiac disorders to proteomic changes. Proteomics Clin Appl 2012; 2:788-99. [PMID: 21136879 DOI: 10.1002/prca.200780076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Myofilament proteins of the cardiac sarcomere house the molecular machinery responsible for generating tension and pressure. Release of intracellular Ca(2+) triggers myofilament tension generation and shortening, but the response to Ca(2+) is modulated by changes in key regulatory proteins. We review how these proteomic changes are essential to adaptive physiological regulation of cardiac output and become maladaptive in cardiac disorders. We also review the essentials of proteomic techniques used to study myofilament protein changes, including degradation, isoform expression, phosphorylation and oxidation. Selected proteomic studies illustrate the applications of these approaches.
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Affiliation(s)
- Chao Yuan
- Department of Physiology and Biophysics and Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, USA
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Wang BH, Reisman S, Bailey M, Kompa A, Ayhan M, Krum H, Rice G. Peptidomic profiles of post myocardial infarction rats affinity depleted plasma using matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) mass spectrometry. Clin Transl Med 2012; 1:11. [PMID: 23369288 PMCID: PMC3560977 DOI: 10.1186/2001-1326-1-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/15/2012] [Indexed: 11/23/2022] Open
Abstract
Background Despite major advances in drug development, effective cardiovascular therapies and suitable cardiovascular biomarkers remain limited. The aim of this study was to leverage mass spectrometry (MS) based peptide profiling strategies to identify changes that occur in peptidomic profiles of rat plasma following coronary artery ligation generated myocardial infarction (MI). Methods One week after MI, rats were randomized to receive either an ACE inhibitor (ramipril, Ram-1 mg/kg/day), or vehicle (Veh) for 12 weeks. Echocardiography and hemodynamic measurements were made before sacrifice and plasma collection. High abundance proteins were depleted with affinity capture before MS profiling. Differentially expressed peptide ions were identified using proprietary software (ClinProtTools). Results MI increased heart/body weight (18%), lung/body weight (56%), and left ventricular (LV) end diastolic pressure (LVEDP, 247%); and significantly reduced percentage fractional shortening (FS, 75%) and rate of pressure rise in the LV (dP/dtmax, 20%). Ram treatment significantly attenuated the changes in LVEDP (61%) and FS (27%). Analysis of MALDI-ToF generated mass spectra demonstrated that peptide ions 1271, 1878, 1955, 2041 and 2254 m/z were consistently decreased by Ram treatment (p < 0.001) and thus may be associated with the agent’s therapeutic effects. Among peptides that were significantly changed, synapsin-2, adenomatous polyposis coli protein and transcription factor jun-D were identified as significantly reduced by Ram treatment. Conclusions This approach allows us to screen for potential biomarkers in a window of the blood proteome that previously has been difficult to access. The data obtained from such an approach may potentially useful in prognosis, diagnosis, and monitoring of treatment response.
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Affiliation(s)
- Bing Hui Wang
- Centre for Clinical Research, University of Queensland, Bld 71/918, Royal Brisbane and Women's Hospital, Herston, QLD, 4032, Australia.
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Gratia S, Kay L, Michelland S, Sève M, Schlattner U, Tokarska-Schlattner M. Cardiac phosphoproteome reveals cell signaling events involved in doxorubicin cardiotoxicity. J Proteomics 2012; 75:4705-16. [PMID: 22348821 DOI: 10.1016/j.jprot.2012.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 02/02/2012] [Accepted: 02/03/2012] [Indexed: 10/14/2022]
Abstract
The successful use of anthracyclines like doxorubicin in chemotherapy is limited by their severe cardiotoxicity. Despite decades of clinical application, a satisfying description of the molecular mechanisms involved and a preventive treatment have not yet been achieved. Here we address doxorubicin-induced changes in cell signaling as a novel potential mediator of doxorubicin toxicity by applying a non-biased screen of the cardiac phosphoproteome. Two-dimensional gel electrophoresis, phosphospecific staining, quantitative image analysis, and MALDI-TOF/TOF mass spectrometry were combined to identify (de)phosphorylation events occurring in the isolated rat heart upon Langendorff-perfusion with clinically relevant (5 μM) and supraclinical concentrations (25 μM) of doxorubicin. This approach identified 22 proteins with a significantly changed phosphorylation status and these results were validated by immunoblotting for selected phosphosites. Overrepresentation of mitochondrial proteins (>40%) identified this compartment as a prime target of doxorubicin. Identified proteins were mainly involved in energy metabolism (e.g. pyruvate dehydrogenase and acyl-CoA dehydrogenase), sarcomere structure and function (e.g. desmin) or chaperone-like activities (e.g. α-crystallin B chain and prohibitin). Changes in phosphorylation of pyruvate dehydrogenase, regulating pyruvate entry into the Krebs cycle, and desmin, maintaining myofibrillar array, are relevant for main symptoms of cardiac dysfunction related to doxorubicin treatment, namely energy imbalance and myofibrillar disorganization. This article is part of a Special Issue entitled: Translational Proteomics.
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Affiliation(s)
- Séverine Gratia
- University Joseph Fourier, Laboratory of Fundamental and Applied Bioenergetics, Environmental and Systems Biology, Grenoble, France
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Didangelos A, Yin X, Mayr M. Method for protein subfractionation of cardiovascular tissues before DIGE analysis. Methods Mol Biol 2012; 854:287-297. [PMID: 22311768 DOI: 10.1007/978-1-61779-573-2_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Difference gel electrophoresis (DIGE) (Electrophoresis 18, 2071-2077, 1997, 1) is widely used in cardiovascular research. However, the dynamic range limitations stemming from contaminating plasma proteins and highly abundant extracellular matrix components can make cardiovascular tissues difficult to analyze. Here we describe a novel methodology for biochemical subfractionation of cardiovascular tissues before DIGE analysis.
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