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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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Reitz CJ, Kuzmanov U, Gramolini AO. Multi-omic analyses and network biology in cardiovascular disease. Proteomics 2023; 23:e2200289. [PMID: 37691071 DOI: 10.1002/pmic.202200289] [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: 03/17/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Heart disease remains a leading cause of death in North America and worldwide. Despite advances in therapies, the chronic nature of cardiovascular diseases ultimately results in frequent hospitalizations and steady rates of mortality. Systems biology approaches have provided a new frontier toward unraveling the underlying mechanisms of cell, tissue, and organ dysfunction in disease. Mapping the complex networks of molecular functions across the genome, transcriptome, proteome, and metabolome has enormous potential to advance our understanding of cardiovascular disease, discover new disease biomarkers, and develop novel therapies. Computational workflows to interpret these data-intensive analyses as well as integration between different levels of interrogation remain important challenges in the advancement and application of systems biology-based analyses in cardiovascular research. This review will focus on summarizing the recent developments in network biology-level profiling in the heart, with particular emphasis on modeling of human heart failure. We will provide new perspectives on integration between different levels of large "omics" datasets, including integration of gene regulatory networks, protein-protein interactions, signaling networks, and metabolic networks in the heart.
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Affiliation(s)
- Cristine J Reitz
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Uros Kuzmanov
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
| | - Anthony O Gramolini
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada
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3
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Herting JR, König JH, Hadova K, Heinick A, Müller FU, Pauls P, Seidl MD, Soppa C, Kirchhefer U. Hypercontractile cardiac phenotype in mice overexpressing the regulatory subunit PR72 of protein phosphatase 2A. Front Cardiovasc Med 2023; 10:1239555. [PMID: 37868783 PMCID: PMC10590119 DOI: 10.3389/fcvm.2023.1239555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Background The activity, localization, and substrate specificity of the protein phosphatase 2A (PP2A) heterotrimer are controlled by various regulatory B subunits. PR72 belongs to the B'' gene family and has been shown to be upregulated in human heart failure. However, little is known about the functions of PR72 in the myocardium. Methods To address this issue, we generated a transgenic mouse model with heart-specific overexpression of PP2A-PR72. Biochemical and physiological methods were used to determine contractility, Ca2+ cycling parameters, and protein phosphorylation. Results A 2.5-fold increase in PR72 expression resulted in moderate cardiac hypertrophy. Maximal ventricular pressure was increased in catheterized transgenic mice (TG) compared to wild-type (WT) littermates. This was accompanied by an increased shortening of sarcomere length and faster relaxation at the single-cell level in TG. In parallel with these findings, the peak amplitude of Ca2+ transients was increased, and the decay in intracellular Ca2+ levels was shortened in TG compared to WT. The changes in Ca2+ cycling in TG were also evident from an increase in the full duration and width at half maximum of Ca2+ sparks. Consistent with the contractile data, phosphorylation of phospholamban at threonine-17 was higher in TG hearts. The lower expression of the Na+/Ca2+ exchanger may also contribute to the hypercontractile state in transgenic myocardium. Conclusion Our results suggest that PP2A-PR72 plays an important role in regulating cardiac contractile function and Ca2+ cycling, indicating that the upregulation of PR72 in heart failure is an attempt to compensate functionally.
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Affiliation(s)
- Julius R. Herting
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Jule H. König
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Katarina Hadova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alexander Heinick
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Frank U. Müller
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Paul Pauls
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Matthias D. Seidl
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Carolina Soppa
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Uwe Kirchhefer
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
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4
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Langa P, Shafaattalab S, Goldspink PH, Wolska BM, Fernandes AA, Tibbits GF, Solaro RJ. A perspective on Notch signalling in progression and arrhythmogenesis in familial hypertrophic and dilated cardiomyopathies. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220176. [PMID: 37122209 PMCID: PMC10150215 DOI: 10.1098/rstb.2022.0176] [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: 09/14/2022] [Accepted: 10/13/2022] [Indexed: 05/02/2023] Open
Abstract
In this perspective, we discussed emerging data indicating a role for Notch signalling in inherited disorders of the heart failure with focus on hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) linked to variants of genes encoding mutant proteins of the sarcomere. We recently reported an upregulation of elements in the Notch signalling cascade in cardiomyocytes derived from human inducible pluripotent stem cells expressing a TNNT2 variant encoding cardiac troponin T (cTnT-I79N+/-), which induces hypertrophy, remodelling, abnormalities in excitation-contraction coupling and electrical instabilities (Shafaattalab S et al. 2021 Front. Cell Dev. Biol. 9, 787581. (doi:10.3389/fcell.2021.787581)). Our search of the literature revealed the novelty of this finding and stimulated us to discuss potential connections between the Notch signalling pathway and familial cardiomyopathies. Our considerations focused on the potential role of these interactions in arrhythmias, microvascular ischaemia, and fibrosis. This finding underscored a need to consider the role of Notch signalling in familial cardiomyopathies which are trigged by sarcomere mutations engaging mechano-signalling pathways for which there is evidence of a role for Notch signalling with crosstalk with Hippo signalling. Our discussion included a role for both cardiac myocytes and non-cardiac myocytes in progression of HCM and DCM. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'.
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Affiliation(s)
- Paulina Langa
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, Chicago, IL, 60612, USA
| | - Sanam Shafaattalab
- Molecular Biology and Biochemistry; BC Children’s Hospital Research Institute, Vancouver, BC, V5Z 4H4; Simon Fraser University Burnaby, British Columbia, V5A 4H4, Canada
| | - Paul H. Goldspink
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, Chicago, IL, 60612, USA
| | - Beata M. Wolska
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, Chicago, IL, 60612, USA
- Department of Medicine, Division of Cardiology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Aurelia A. Fernandes
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, Chicago, IL, 60612, USA
| | - Glen F. Tibbits
- Molecular Biology and Biochemistry; BC Children’s Hospital Research Institute, Vancouver, BC, V5Z 4H4; Simon Fraser University Burnaby, British Columbia, V5A 4H4, Canada
| | - R. John Solaro
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, Chicago, IL, 60612, USA
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5
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Tan Y, Lu T, Chen Y, Witman N, Yan B, Yang L, Liu M, Gong Y, Ai X, Luo R, Wang H, Wang W, Fu W. Engineering a conduction-consistent cardiac patch with graphene oxide modified butterfly wings and human pluripotent stem cell-derived cardiomyocytes. Bioeng Transl Med 2023; 8:e10522. [PMID: 37206241 PMCID: PMC10189447 DOI: 10.1002/btm2.10522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 03/12/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023] Open
Abstract
Engineering a conduction-consistent cardiac patch has direct implications to biomedical research. However, there is difficulty in obtaining and maintaining a system that allows researchers to study physiologically relevant cardiac development, maturation, and drug screening due to the issues around inconsistent contractions of cardiomyocytes. Butterfly wings have special nanostructures arranged in parallel, which could help generate the alignment of cardiomyocytes to better mimic the natural heart tissue structure. Here, we construct a conduction-consistent human cardiac muscle patch by assembling human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) on graphene oxide (GO) modified butterfly wings. We also show this system functions as a versatile model to study human cardiomyogenesis by assembling human induced pluripotent stem cell-derived cardiac progenitor cells (hiPSC-CPCs) on the GO modified butterfly wings. The GO modified butterfly wing platform facilitated the parallel orientation of hiPSC-CMs, enhanced relative maturation as well as improved conduction consistency of the cardiomyocytes. In addition, GO modified butterfly wings enhanced the proliferation and maturation characteristics of the hiPSC-CPCs. In accordance with data obtained from RNA-sequencing and gene signatures, assembling hiPSC-CPCs on GO modified butterfly wings stimulated the differentiation of the progenitors into relatively mature hiPSC-CMs. These characteristics and capabilities of GO modified butterfly wings make them an ideal platform for heart research and drug screening.
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Affiliation(s)
- Yao Tan
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Tingting Lu
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Ying Chen
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Nevin Witman
- Department of Clinical NeuroscienceKarolinska InstitutetStockholmSweden
| | - Bingqian Yan
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Li Yang
- Department of AnesthesiologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Minglu Liu
- Department of Pediatric Cardiothoracic SurgeryShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yiqi Gong
- Department of Pediatric Cardiothoracic SurgeryShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Xuefeng Ai
- Department of Pediatric Cardiothoracic SurgeryShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Runjiao Luo
- Department of Pediatric Cardiothoracic SurgeryShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Huijing Wang
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Wei Wang
- Department of Pediatric Cardiothoracic SurgeryShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Wei Fu
- Institute of Pediatric Translational MedicineShanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Tissue EngineeringShanghai 9th People's Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
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6
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Valero-Muñoz M, Saw EL, Hekman RM, Blum BC, Hourani Z, Granzier H, Emili A, Sam F. Proteomic and phosphoproteomic profiling in heart failure with preserved ejection fraction (HFpEF). Front Cardiovasc Med 2022; 9:966968. [PMID: 36093146 PMCID: PMC9452734 DOI: 10.3389/fcvm.2022.966968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Although the prevalence of heart failure with preserved ejection fraction (HFpEF) is increasing, evidence-based therapies for HFpEF remain limited, likely due to an incomplete understanding of this disease. This study sought to identify the cardiac-specific features of protein and phosphoprotein changes in a murine model of HFpEF using mass spectrometry. HFpEF mice demonstrated moderate hypertension, left ventricle (LV) hypertrophy, lung congestion and diastolic dysfunction. Proteomics analysis of the LV tissue showed that 897 proteins were differentially expressed between HFpEF and Sham mice. We observed abundant changes in sarcomeric proteins, mitochondrial-related proteins, and NAD-dependent protein deacetylase sirtuin-3 (SIRT3). Upregulated pathways by GSEA analysis were related to immune modulation and muscle contraction, while downregulated pathways were predominantly related to mitochondrial metabolism. Western blot analysis validated SIRT3 downregulated cardiac expression in HFpEF vs. Sham (0.8 ± 0.0 vs. 1.0 ± 0.0; P < 0.001). Phosphoproteomics analysis showed that 72 phosphosites were differentially regulated between HFpEF and Sham LV. Aberrant phosphorylation patterns mostly occurred in sarcomere proteins and nuclear-localized proteins associated with contractile dysfunction and cardiac hypertrophy. Seven aberrant phosphosites were observed at the z-disk binding region of titin. Additional agarose gel analysis showed that while total titin cardiac expression remained unaltered, its stiffer N2B isoform was significantly increased in HFpEF vs. Sham (0.144 ± 0.01 vs. 0.127 ± 0.01; P < 0.05). In summary, this study demonstrates marked changes in proteins related to mitochondrial metabolism and the cardiac contractile apparatus in HFpEF. We propose that SIRT3 may play a role in perpetuating these changes and may be a target for drug development in HFpEF.
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Affiliation(s)
- María Valero-Muñoz
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
- *Correspondence: María Valero-Muñoz,
| | - Eng Leng Saw
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
| | - Ryan M. Hekman
- Department of Biology, Boston University, Boston, MA, United States
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
| | - Benjamin C. Blum
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
- Center for Network Systems Biology, Boston University, Boston, MA, United States
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, United States
| | - Andrew Emili
- Department of Biology, Boston University, Boston, MA, United States
- Department of Biochemistry, Cell Biology and Genomics, Boston University, Boston, MA, United States
| | - Flora Sam
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
- Flora Sam,
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7
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Sorrentino A, Bagwan N, Linscheid N, Poulsen PC, Kahnert K, Thomsen MB, Delmar M, Lundby A. Beta-blocker/ACE inhibitor therapy differentially impacts the steady state signaling landscape of failing and non-failing hearts. Sci Rep 2022; 12:4760. [PMID: 35306519 PMCID: PMC8934364 DOI: 10.1038/s41598-022-08534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
Heart failure is a multifactorial disease that affects an estimated 38 million people worldwide. Current pharmacotherapy of heart failure with reduced ejection fraction (HFrEF) includes combination therapy with angiotensin-converting enzyme inhibitors (ACEi) and β-adrenergic receptor blockers (β-AR blockers), a therapy also used as treatment for non-cardiac conditions. Our knowledge of the molecular changes accompanying treatment with ACEi and β-AR blockers is limited. Here, we applied proteomics and phosphoproteomics approaches to profile the global changes in protein abundance and phosphorylation state in cardiac left ventricles consequent to combination therapy of β-AR blocker and ACE inhibitor in HFrEF and control hearts. The phosphorylation changes induced by treatment were profoundly different for failing than for non-failing hearts. HFrEF was characterized by profound downregulation of mitochondrial proteins coupled with derangement of β-adrenergic and pyruvate dehydrogenase signaling. Upon treatment, phosphorylation changes consequent to HFrEF were reversed. In control hearts, treatment mainly led to downregulation of canonical PKA signaling. The observation of divergent signaling outcomes depending on disease state underscores the importance of evaluating drug effects within the context of the specific conditions present in the recipient heart.
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8
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Moore J, Emili A. Mass-Spectrometry-Based Functional Proteomic and Phosphoproteomic Technologies and Their Application for Analyzing Ex Vivo and In Vitro Models of Hypertrophic Cardiomyopathy. Int J Mol Sci 2021; 22:13644. [PMID: 34948439 PMCID: PMC8709159 DOI: 10.3390/ijms222413644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease thought to be principally caused by mutations in sarcomeric proteins. Despite extensive genetic analysis, there are no comprehensive molecular frameworks for how single mutations in contractile proteins result in the diverse assortment of cellular, phenotypic, and pathobiological cascades seen in HCM. Molecular profiling and system biology approaches are powerful tools for elucidating, quantifying, and interpreting dynamic signaling pathways and differential macromolecule expression profiles for a wide range of sample types, including cardiomyopathy. Cutting-edge approaches combine high-performance analytical instrumentation (e.g., mass spectrometry) with computational methods (e.g., bioinformatics) to study the comparative activity of biochemical pathways based on relative abundances of functionally linked proteins of interest. Cardiac research is poised to benefit enormously from the application of this toolkit to cardiac tissue models, which recapitulate key aspects of pathogenesis. In this review, we evaluate state-of-the-art mass-spectrometry-based proteomic and phosphoproteomic technologies and their application to in vitro and ex vivo models of HCM for global mapping of macromolecular alterations driving disease progression, emphasizing their potential for defining the components of basic biological systems, the fundamental mechanistic basis of HCM pathogenesis, and treating the ensuing varied clinical outcomes seen among affected patient cohorts.
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Affiliation(s)
- Jarrod Moore
- Center for Network Systems Biology, Boston University School of Medicine, Boston, MA 02118, USA;
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
- MD-PhD Program, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University School of Medicine, Boston, MA 02118, USA;
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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9
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Vahabi N, McDonough CW, Desai AA, Cavallari LH, Duarte JD, Michailidis G. Cox-sMBPLS: An Algorithm for Disease Survival Prediction and Multi-Omics Module Discovery Incorporating Cis-Regulatory Quantitative Effects. Front Genet 2021; 12:701405. [PMID: 34408773 PMCID: PMC8366414 DOI: 10.3389/fgene.2021.701405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/07/2021] [Indexed: 12/03/2022] Open
Abstract
Background The development of high-throughput techniques has enabled profiling a large number of biomolecules across a number of molecular compartments. The challenge then becomes to integrate such multimodal Omics data to gain insights into biological processes and disease onset and progression mechanisms. Further, given the high dimensionality of such data, incorporating prior biological information on interactions between molecular compartments when developing statistical models for data integration is beneficial, especially in settings involving a small number of samples. Results We develop a supervised model for time to event data (e.g., death, biochemical recurrence) that simultaneously accounts for redundant information within Omics profiles and leverages prior biological associations between them through a multi-block PLS framework. The interactions between data from different molecular compartments (e.g., epigenome, transcriptome, methylome, etc.) were captured by using cis-regulatory quantitative effects in the proposed model. The model, coined Cox-sMBPLS, exhibits superior prediction performance and improved feature selection based on both simulation studies and analysis of data from heart failure patients. Conclusion The proposed supervised Cox-sMBPLS model can effectively incorporate prior biological information in the survival prediction system, leading to improved prediction performance and feature selection. It also enables the identification of multi-Omics modules of biomolecules that impact the patients’ survival probability and also provides insights into potential relevant risk factors that merit further investigation.
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Affiliation(s)
- Nasim Vahabi
- Informatics Institute, University of Florida, Gainesville, FL, United States
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - Ankit A Desai
- Department of Medicine, Indiana University, Indianapolis, IN, United States
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - Julio D Duarte
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - George Michailidis
- Informatics Institute, University of Florida, Gainesville, FL, United States
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10
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Kwon HK, Choi H, Park SG, Park WJ, Kim, DH, Park ZY. Integrated Quantitative Phosphoproteomics and Cell-based Functional Screening Reveals Specific Pathological Cardiac Hypertrophy-related Phosphorylation Sites. Mol Cells 2021; 44:500-516. [PMID: 34158421 PMCID: PMC8334354 DOI: 10.14348/molcells.2021.4002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
Cardiac hypertrophic signaling cascades resulting in heart failure diseases are mediated by protein phosphorylation. Recent developments in mass spectrometry-based phosphoproteomics have led to the identification of thousands of differentially phosphorylated proteins and their phosphorylation sites. However, functional studies of these differentially phosphorylated proteins have not been conducted in a large-scale or high-throughput manner due to a lack of methods capable of revealing the functional relevance of each phosphorylation site. In this study, an integrated approach combining quantitative phosphoproteomics and cell-based functional screening using phosphorylation competition peptides was developed. A pathological cardiac hypertrophy model, junctate-1 transgenic mice and control mice, were analyzed using label-free quantitative phosphoproteomics to identify differentially phosphorylated proteins and sites. A cell-based functional assay system measuring hypertrophic cell growth of neonatal rat ventricle cardiomyocytes (NRVMs) following phenylephrine treatment was applied, and changes in phosphorylation of individual differentially phosphorylated sites were induced by incorporation of phosphorylation competition peptides conjugated with cell-penetrating peptides. Cell-based functional screening against 18 selected phosphorylation sites identified three phosphorylation sites (Ser-98, Ser-179 of Ldb3, and Ser-1146 of palladin) displaying near-complete inhibition of cardiac hypertrophic growth of NRVMs. Changes in phosphorylation levels of Ser-98 and Ser-179 in Ldb3 were further confirmed in NRVMs and other pathological/physiological hypertrophy models, including transverse aortic constriction and swimming models, using site-specific phospho-antibodies. Our integrated approach can be used to identify functionally important phosphorylation sites among differentially phosphorylated sites, and unlike conventional approaches, it is easily applicable for large-scale and/or high-throughput analyses.
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Affiliation(s)
- Hye Kyeong Kwon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyunwoo Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Sung-Gyoo Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Woo Jin Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Do Han Kim,
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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11
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Quantitative proteome comparison of human hearts with those of model organisms. PLoS Biol 2021; 19:e3001144. [PMID: 33872299 PMCID: PMC8084454 DOI: 10.1371/journal.pbio.3001144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/29/2021] [Accepted: 02/12/2021] [Indexed: 01/23/2023] Open
Abstract
Delineating human cardiac pathologies and their basic molecular mechanisms relies on research conducted in model organisms. Yet translating findings from preclinical models to humans present a significant challenge, in part due to differences in cardiac protein expression between humans and model organisms. Proteins immediately determine cellular function, yet their large-scale investigation in hearts has lagged behind those of genes and transcripts. Here, we set out to bridge this knowledge gap: By analyzing protein profiles in humans and commonly used model organisms across cardiac chambers, we determine their commonalities and regional differences. We analyzed cardiac tissue from each chamber of human, pig, horse, rat, mouse, and zebrafish in biological replicates. Using mass spectrometry–based proteomics workflows, we measured and evaluated the abundance of approximately 7,000 proteins in each species. The resulting knowledgebase of cardiac protein signatures is accessible through an online database: atlas.cardiacproteomics.com. Our combined analysis allows for quantitative evaluation of protein abundances across cardiac chambers, as well as comparisons of cardiac protein profiles across model organisms. Up to a quarter of proteins with differential abundances between atria and ventricles showed opposite chamber-specific enrichment between species; these included numerous proteins implicated in cardiac disease. The generated proteomics resource facilitates translational prospects of cardiac studies from model organisms to humans by comparisons of disease-linked protein networks across species. This study provides protein abundance profiles for thousands of proteins across cardiac chambers for humans and five commonly used model organisms. This quantitative proteomics dataset represents the most comprehensive such resource to date, and can be queried via a web browser to identify the most appropriate model organism for future studies.
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12
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Lee SH, Kim DH, Kuzmanov U, Gramolini AO. Membrane proteomic profiling of the heart: past, present, and future. Am J Physiol Heart Circ Physiol 2020; 320:H417-H423. [PMID: 33185114 DOI: 10.1152/ajpheart.00659.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cardiovascular diseases remain the most rapidly rising contributing factor of all-cause mortality and the leading cause of inpatient hospitalization worldwide, with costs exceeding $30 billion annually in North America. Cell surface and membrane-associated proteins play an important role in cardiomyocyte biology and are involved in the pathogenesis of many human heart diseases. In cardiomyocytes, membrane proteins serve as critical signaling receptors, Ca2+ cycling regulators, and electrical propagation regulators, all functioning in concert to maintain spontaneous and synchronous contractions of cardiomyocytes. Membrane proteins are excellent pharmaceutical targets due to their uniquely exposed position within the cell. Perturbations in cardiac membrane protein localization and function have been implicated in the progression and pathogenesis of many heart diseases. However, previous attempts at profiling the cardiac membrane proteome have yielded limited results due to poor technological developments for isolating hydrophobic, low-abundance membrane proteins. Comprehensive mapping and characterization of the cardiac membrane proteome thereby remains incomplete. This review will focus on recent advances in mapping the cardiac membrane proteome and the role of novel cardiac membrane proteins in the healthy and the diseased heart.
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Affiliation(s)
- Shin-Haw Lee
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Da Hye Kim
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Uros Kuzmanov
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anthony O Gramolini
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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13
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Plasma Proteome Profiling of Coronary Artery Disease Patients: Downregulation of Transthyretin-An Important Event. Mediators Inflamm 2020; 2020:3429541. [PMID: 33299376 PMCID: PMC7707994 DOI: 10.1155/2020/3429541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023] Open
Abstract
Coronary artery disease (CAD) is a prevalent chronic inflammatory cardiac disorder. An early diagnosis is likely to help in the prevention and proper management of this disease. As the study of proteomics provides the potential markers for detection of a disease, in the present investigation, attempt has been made to identify disease-associated differential proteins involved in CAD pathogenesis. For this study, a total of 200 selected CAD patients were considered, who were recruited for percutaneous coronary intervention (PCI) treatment. The proteomic analysis was performed using two-dimensional gel electrophoresis (2-DE) and MALDI-TOF MS/MS. Samples were also subjected to Western blot analysis, enzyme-linked immunosorbent assay (ELISA), peripheral blood mononuclear cells isolation immunofluorescence (IF) analysis, analytical screening by fluorescence-activated cell sorting (FACS), and in silico analysis. The representative data were shown as mean ± SD of at least three experiments. A total of 19 proteins were identified. Among them, the most abundant five proteins (serotransferrin, talin-1, alpha-2HS glycoprotein, transthyretin (TTR), fibrinogen-α chain) were found to have altered level in CAD. Serotransferrin, talin-1, alpha-2HS glycoprotein, and transthyretin (TTR) were found to have lower level, whereas fibrinogen-α chain was found to have higher level in CAD plasma compared to healthy, confirmed by Western blot analysis. TTR, an important acute phase transport protein, was validated low level in 200 CAD patients who confirmed to undergo PCI treatment. Further, in silico and in vitro studies of TTR indicated a downexpression of CAD in plasma as compared to the plasma of healthy individuals. Lower level of plasma TTR was determined to be an important risk marker in the atherosclerotic-approved CAD patients. We suggest that the TTR lower level predicts disease severity and hence may serve as an important marker tool for CAD screening. However, further large-scale studies are required to determine the clinical significance of TTR.
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14
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Mapping signalling perturbations in myocardial fibrosis via the integrative phosphoproteomic profiling of tissue from diverse sources. Nat Biomed Eng 2020; 4:889-900. [PMID: 32661320 DOI: 10.1038/s41551-020-0585-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/14/2020] [Indexed: 12/13/2022]
Abstract
Study of the molecular basis of myocardial fibrosis is hampered by limited access to tissues from human patients and by confounding variables associated with sample accessibility, collection, processing and storage. Here, we report an integrative strategy based on mass spectrometry for the phosphoproteomic profiling of normal and fibrotic cardiac tissue obtained from surgical explants from patients with hypertrophic cardiomyopathy, from a transaortic-constriction mouse model of cardiac hypertrophy and fibrosis, and from a heart-on-a-chip model of cardiac fibrosis. We used the integrative approach to map the relative abundance of thousands of proteins, phosphoproteins and phosphorylation sites specific to each tissue source, to identify key signalling pathways driving fibrosis and to screen for anti-fibrotic compounds targeting glycogen synthase kinase 3, which has a consistent role as a key mediator of fibrosis in all three types of tissue specimen. The integrative disease-modelling strategy may reveal new insights into mechanisms of cardiac disease and serve as a test bed for drug screening.
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15
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Wozniak JM, Silva TA, Thomas D, Siqueira-Neto JL, McKerrow JH, Gonzalez DJ, Calvet CM. Molecular dissection of Chagas induced cardiomyopathy reveals central disease associated and druggable signaling pathways. PLoS Negl Trop Dis 2020; 14:e0007980. [PMID: 32433643 PMCID: PMC7279607 DOI: 10.1371/journal.pntd.0007980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/08/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Chagas disease, the clinical presentation of T. cruzi infection, is a major human health concern. While the acute phase of Chagas disease is typically asymptomatic and self-resolving, chronically infected individuals suffer numerous sequelae later in life. Cardiomyopathies in particular are the most severe consequence of chronic Chagas disease and cannot be reversed solely by parasite load reduction. To prioritize new therapeutic targets, we unbiasedly interrogated the host signaling events in heart tissues isolated from a Chagas disease mouse model using quantitative, multiplexed proteomics. We defined the host response to infection at both the proteome and phospho-proteome levels. The proteome showed an increase in the immune response and a strong repression of several mitochondrial proteins. Complementing the proteome studies, the phospho-proteomic survey found an abundance of phospho-site alterations in plasma membrane and cytoskeletal proteins. Bioinformatic analysis of kinase activity provided substantial evidence for the activation of NDRG2 and JNK/p38 kinases during Chagas disease. A significant activation of DYRK2 and AMPKA2 and the inhibition of casein family kinases were also predicted. We concluded our analyses by linking the diseased heart proteome profile to known therapeutic interventions, uncovering a potential to target mitochondrial proteins, secreted immune effectors and core kinases for the treatment of chronic Chagas disease. Together, this study provides molecular insight into host proteome and phospho-proteome responses to T. cruzi infection in the heart for the first time, highlighting pathways that can be further validated for functional contributions to disease and suitability as drug targets.
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Affiliation(s)
- Jacob M. Wozniak
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Department of Pharmacology; University of California San Diego; La Jolla, CA, United States of America
| | - Tatiana Araújo Silva
- Cellular Ultrastructure Laboratory; Oswaldo Cruz Institute, FIOCRUZ; Rio de Janeiro, RJ, Brazil
| | - Diane Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - David J. Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Department of Pharmacology; University of California San Diego; La Jolla, CA, United States of America
- * E-mail: (DJG); (CMC)
| | - Claudia M. Calvet
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Cellular Ultrastructure Laboratory; Oswaldo Cruz Institute, FIOCRUZ; Rio de Janeiro, RJ, Brazil
- * E-mail: (DJG); (CMC)
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16
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Ramachandran CD, Gholami K, Lam SK, Hoe SZ. A preliminary study of the effect of a high-salt diet on transcriptome dynamics in rat hypothalamic forebrain and brainstem cardiovascular control centers. PeerJ 2020; 8:e8528. [PMID: 32175184 PMCID: PMC7059759 DOI: 10.7717/peerj.8528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/07/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND High dietary salt intake is strongly correlated with cardiovascular (CV) diseases and it is regarded as a major risk factor associated with the pathogenesis of hypertension. The CV control centres in the brainstem (the nucleus tractus solitarii (NTS) and the rostral ventrolateral medulla (RVLM)) and hypothalamic forebrain (the subfornical organ, SFO; the supraoptic nucleus, SON and the paraventricular nucleus, PVN) have critical roles in regulating CV autonomic motor outflows, and thus maintaining blood pressure (BP). Growing evidence has implicated autonomic regulatory networks in salt-sensitive HPN (SSH), but the genetic basis remains to be delineated. We hypothesized that the development and/ or maintenance of SSH is reliant on the change in the expression of genes in brain regions controlling the CV system. METHODOLOGY We used RNA-Sequencing (RNA-Seq) to describe the differential expression of genes in SFO, SON, PVN, NTS and RVLM of rats being chronically fed with high-salt (HS) diet. Subsequently, a selection of putatively regulated genes was validated with quantitative reverse transcription polymerase chain reaction (qRT-PCR) in both Spontaneously Hypertensive rats (SHRs) and Wistar Kyoto (WKY) rats. RESULTS The findings enabled us to identify number of differentially expressed genes in SFO, SON, PVN, NTS and RVLM; that are either up-regulated in both strains of rats (SON- Caprin2, Sctr), down-regulated in both strains of rats (PVN- Orc, Gkap1), up-regulated only in SHRs (SFO- Apopt1, Lin52, AVP, OXT; SON- AVP, OXT; PVN- Caprin2, Sclt; RVLM- A4galt, Slc29a4, Cmc1) or down-regulated only in SHRs (SON- Ndufaf2, Kcnv1; PVN- Pi4k2a; NTS- Snrpd2l, Ankrd29, St6galnac6, Rnf157, Iglon5, Csrnp3, Rprd1a; RVLM- Ttr, Faim). CONCLUSIONS These findings demonstrated the adverse effects of HS diet on BP, which may be mediated via modulating the signaling systems in CV centers in the hypothalamic forebrain and brainstem.
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Affiliation(s)
- Chitra Devi Ramachandran
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Perseketuan, Malaysia
| | - Khadijeh Gholami
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Perseketuan, Malaysia
- Human Biology Division, School of Medicine, International Medical University, Kuala Lumpur, Wilayah Perseketuan, Malaysia
| | - Sau Kuen Lam
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Perseketuan, Malaysia
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sungai Long, Selangor, Malaysia
| | - See Ziau Hoe
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Perseketuan, Malaysia
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17
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REEP5 depletion causes sarco-endoplasmic reticulum vacuolization and cardiac functional defects. Nat Commun 2020; 11:965. [PMID: 32075961 PMCID: PMC7031342 DOI: 10.1038/s41467-019-14143-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The sarco-endoplasmic reticulum (SR/ER) plays an important role in the development and progression of many heart diseases. However, many aspects of its structural organization remain largely unknown, particularly in cells with a highly differentiated SR/ER network. Here, we report a cardiac enriched, SR/ER membrane protein, REEP5 that is centrally involved in regulating SR/ER organization and cellular stress responses in cardiac myocytes. In vitro REEP5 depletion in mouse cardiac myocytes results in SR/ER membrane destabilization and luminal vacuolization along with decreased myocyte contractility and disrupted Ca2+ cycling. Further, in vivo CRISPR/Cas9-mediated REEP5 loss-of-function zebrafish mutants show sensitized cardiac dysfunction upon short-term verapamil treatment. Additionally, in vivo adeno-associated viral (AAV9)-induced REEP5 depletion in the mouse demonstrates cardiac dysfunction. These results demonstrate the critical role of REEP5 in SR/ER organization and function as well as normal heart function and development. The sarcoplasmic (SR) and endoplasmic reticulum (ER) are involved in heart development but how this arises is unclear. Here, the authors show that loss of a SR/ER protein REEP5 causes membrane destabilization and decreased cardiac myocyte contractility, with cardiac dysfunction in mutant mouse and zebrafish models.
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18
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Tang J, Wang Y, Li Y, Zhang Y, Zhang R, Xiao Z, Luo Y, Guo X, Tao L, Lou Y, Xue W, Zhu F. Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics. Curr Pharm Des 2019; 25:1536-1553. [PMID: 31258068 DOI: 10.2174/1381612825666190618123306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yang Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Runyuan Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Ziyu Xiao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Xueying Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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Callaghan NI, Hadipour-Lakmehsari S, Lee SH, Gramolini AO, Simmons CA. Modeling cardiac complexity: Advancements in myocardial models and analytical techniques for physiological investigation and therapeutic development in vitro. APL Bioeng 2019; 3:011501. [PMID: 31069331 PMCID: PMC6481739 DOI: 10.1063/1.5055873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/31/2018] [Indexed: 02/06/2023] Open
Abstract
Cardiomyopathies, heart failure, and arrhythmias or conduction blockages impact millions of patients worldwide and are associated with marked increases in sudden cardiac death, decline in the quality of life, and the induction of secondary pathologies. These pathologies stem from dysfunction in the contractile or conductive properties of the cardiomyocyte, which as a result is a focus of fundamental investigation, drug discovery and therapeutic development, and tissue engineering. All of these foci require in vitro myocardial models and experimental techniques to probe the physiological functions of the cardiomyocyte. In this review, we provide a detailed exploration of different cell models, disease modeling strategies, and tissue constructs used from basic to translational research. Furthermore, we highlight recent advancements in imaging, electrophysiology, metabolic measurements, and mechanical and contractile characterization modalities that are advancing our understanding of cardiomyocyte physiology. With this review, we aim to both provide a biological framework for engineers contributing to the field and demonstrate the technical basis and limitations underlying physiological measurement modalities for biologists attempting to take advantage of these state-of-the-art techniques.
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Affiliation(s)
| | | | | | | | - Craig A. Simmons
- Author to whom correspondence should be addressed: . Present address: Ted Rogers Centre for Heart
Research, 661 University Avenue, 14th Floor Toronto, Ontario M5G 1M1, Canada. Tel.:
416-946-0548. Fax: 416-978-7753
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20
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Li SM, Liu WT, Yang F, Yi QJ, Zhang S, Jia HL. Phosphorylated proteomics analysis of human coronary artery endothelial cells stimulated by Kawasaki disease patients serum. BMC Cardiovasc Disord 2019; 19:21. [PMID: 30654760 PMCID: PMC6337789 DOI: 10.1186/s12872-018-0982-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 12/17/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Kawasaki disease (KD) is an acute febrile childhood systemic vasculitis that disturbs coronary arteries. The pathogenesis remains unknown. The study of phosphorylated proteins helps to elucidate the relevant pathophysiological mechanisms of cardiovascular disease. However, few researches explored phosphorylated proteins in KD patients. METHODS We compared phosphoprotein profiles of HCAECs stimulated by the serum of KD patients and normal children using iTRAQ technology, TiO2 enrichment phosphorylated peptide and MS analysis. Then we conducted the functional analysis by ClueGO and the biological interaction networking analysis by ReactomeFIViz. Western blotting was performed to identify the hub proteins. RESULTS Our results revealed that phosphorylation of 148 proteins showed different intensities between the two HCAECs groups, which are enriched in MAPK, VEGFR, EGFR, Angiopoietin receptor, mTOR, FAK signaling pathway and so on. Through the Network Analyzer analysis, the hub proteins are CDKN1A, MAPK1 and POLR2A, which were experimentally validated. CONCLUSION In summary, we provided evidence addressing the valuable phosphorylation signaling that could be useful resource to understand the molecular mechanism and the potential targets for novel therapy of KD.
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Affiliation(s)
- Shui-Ming Li
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Wan-Ting Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
| | - Fang Yang
- Department of Pediatrics, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qi-Jian Yi
- Department of Cardiovascular Medicine, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child development and Disorder, China International Science and Technology Coorperation base of Child development and Critical Disorder, Chongqing Key Laboratory of Pediatrics, Chongqing, China.
| | - Shuai Zhang
- Department of Medical Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jinan University, Guangzhou, Guangdong, China.
| | - Hong-Ling Jia
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China.
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21
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Nomura S. Genetic and non-genetic determinants of clinical phenotypes in cardiomyopathy. J Cardiol 2018; 73:187-190. [PMID: 30527532 DOI: 10.1016/j.jjcc.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022]
Abstract
Cardiomyopathy, a leading cause of death worldwide, is etiologically and phenotypically heterogeneous and is caused by a combination of genetic and non-genetic factors. Major genomic determinants of dilated cardiomyopathy (DCM) are titin truncating mutations and lamin A/C mutations. Patients with these two genotypes show critically different phenotypes, including penetrance, coexistence with a conduction system abnormality, cardiac prognosis, and treatment response. The transcriptomic and epigenomic characteristics of DCM include activation of the DNA damage response, metabolic reprogramming, and dedifferentiation. The proteomic and metabolomic signatures of the DCM heart include a rigorous dependency for free fatty acids, activation of the stress response, and metabolic reprogramming. Proteomic and metabolomic analyses of blood show a distinct immune response and an unexpected link with pathology-specific microbiota in DCM. The direct integration of multi-omics data will not only elucidate inter-omics associations but also enable omics-based patient stratification, which will lead to a deeper understanding of cardiomyopathy and the development of precision medicine in cardiology.
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Affiliation(s)
- Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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22
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Qureshi AP, Stachler MD, Haque O, Odze RD. Biomarkers for Barrett's esophagus - a contemporary review. Expert Rev Mol Diagn 2018; 18:939-946. [PMID: 30345836 DOI: 10.1080/14737159.2018.1538793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Esophageal adenocarcinoma (EAC) has a poor 5-year survival rate (10%-18%), and incidence has increased dramatically in the past three decades. Barrett's esophagus (BE) is the precursor lesion to EAC and is the replacement of the normally squamous lined esophagus with columnar cells that develop an intestinal phenotype characterized by the presence of goblet cells. Given the known precursor state, EAC is amenable to screening and surveillance strategies (analogous to colon cancer). However, unlike from colon cancer screening, BE poses challenges that make effective screening difficult. Robust and concerted effort is under way to find biomarkers of BE. Areas covered: This review summarizes current known biomarkers for BE. These include dysplasia, genomic markers, and gene expression alterations that occur early in the dysplasia/carcinoma sequence. Expert commentary: Despite the tremendous breadth of work in studying molecular advances, the ideal biomarker for BE has not yet been discerned. This review comments on innovations in the field of BE research that combine state-of-the-art molecular advances with simple technologies.
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Affiliation(s)
- Alia P Qureshi
- a Beth Israel Deaconess Medical Center, Department of Surgery , Harvard Medical School , Boston , MA
| | - Matthew D Stachler
- b Department of Pathology, Harvard Medical School , Brigham and Women's Hospital , Boston , MA
| | - Omar Haque
- a Beth Israel Deaconess Medical Center, Department of Surgery , Harvard Medical School , Boston , MA
| | - Robert D Odze
- b Department of Pathology, Harvard Medical School , Brigham and Women's Hospital , Boston , MA
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23
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Stachowski MJ, Holewinski RJ, Grote E, Venkatraman V, Van Eyk JE, Kirk JA. Phospho-Proteomic Analysis of Cardiac Dyssynchrony and Resynchronization Therapy. Proteomics 2018; 18:e1800079. [PMID: 30129105 DOI: 10.1002/pmic.201800079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/09/2018] [Indexed: 12/15/2022]
Abstract
Cardiac dyssynchrony arises from conduction abnormalities during heart failure and worsens morbidity and mortality. Cardiac resynchronization therapy (CRT) re-coordinates contraction using bi-ventricular pacing, but the cellular and molecular mechanisms involved remain largely unknown. The aim is to determine how dyssynchronous heart failure (HFdys ) alters the phospho-proteome and how CRT interacts with this unique phospho-proteome by analyzing Ser/Thr and Tyr phosphorylation. Phospho-enriched myocardium from dog models of Control, HFdys , and CRT is analyzed via MS. There were 209 regulated phospho-sites among 1761 identified sites. Compared to Con and CRT, HFdys is hyper-phosphorylated and tyrosine phosphorylation is more likely to be involved in signaling that increased with HFdys and was exacerbated by CRT. For each regulated site, the most-likely targeting-kinase is predicted, and CK2 is highly specific for sites that are "fixed" by CRT, suggesting activation of CK2 signaling occurs in HFdys that is reversed by CRT, which is supported by western blot analysis. These data elucidate signaling networks and kinases that may be involved and deserve further study. Importantly, a possible role for CK2 modulation in CRT has been identified. This may be harnessed in the future therapeutically to compliment CRT, improving its clinical effects.
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Affiliation(s)
- Marisa J Stachowski
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Ronald J Holewinski
- Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, 90048, USA
| | - Eric Grote
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, 90048, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, 90048, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jonathan A Kirk
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
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24
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Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE. Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Proteome Sci 2018; 16:16. [PMID: 30140170 PMCID: PMC6098843 DOI: 10.1186/s12953-018-0143-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/19/2018] [Indexed: 01/27/2023] Open
Abstract
Background The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolutionarily conserved relative of the Src family kinases (SFKs). Tyrosine kinases are known to regulate a number of cellular processes and pathways via phosphorylating substrate proteins directly and/or by partaking in signaling cross-talks leading to the indirect modulation of various signaling intermediates. In a previous study, we profiled the tyrosine-phosphoproteome of SRMS and identified multiple candidate substrates of the kinase. The broader cellular signaling intermediates of SRMS are unknown. Methods In order to uncover the broader SRMS-regulated phosphoproteome and identify the SRMS-regulated indirect signaling intermediates, we performed label-free global phosphoproteomics analysis on cells expressing wild-type SRMS. Using computational database searching and bioinformatics analyses we characterized the dataset. Results Our analyses identified 60 hyperphosphorylated (phosphoserine/phosphothreonine) proteins mapped from 140 hyperphosphorylated peptides. Bioinfomatics analyses identified a number of significantly enriched biological and cellular processes among which DNA repair pathways were found to be upregulated while apoptotic pathways were found to be downregulated. Analyses of motifs derived from the upregulated phosphosites identified Casein kinase 2 alpha (CK2α) as one of the major potential kinases contributing to the SRMS-dependent indirect regulation of signaling intermediates. Conclusions Overall, our phosphoproteomics analyses identified serine/threonine phosphorylation dynamics as important secondary events of the SRMS-regulated phosphoproteome with implications in the regulation of cellular and biological processes. Electronic supplementary material The online version of this article (10.1186/s12953-018-0143-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raghuveera Kumar Goel
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - Mona Meyer
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Marta Paczkowska
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada
| | - Jüri Reimand
- 2Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3 Canada.,3Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON M5G 1L7 Canada
| | - Frederick Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Franco Vizeacoumar
- 4Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada.,5Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
| | - TuKiet T Lam
- 6Department of Molecular Biophysics and Biochemistry and MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT USA
| | - Kiven Erique Lukong
- 1Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada
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25
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Sun L, Lin C, Li X, Xing L, Huo D, Sun J, Zhang L, Yang H. Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers. Front Physiol 2018; 9:836. [PMID: 30018572 PMCID: PMC6037860 DOI: 10.3389/fphys.2018.00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/14/2018] [Indexed: 12/29/2022] Open
Abstract
Sea cucumbers exposed to stressful circumstances eviscerate most internal organs, and then regenerate them rapidly under favorable environments. Reversible protein phosphorylation and acetylation are major modifications regulating protein function. Herein, for the first time, we perform quantitative phospho- and acetyl proteomics analyses of intestine regeneration in a sea cucumber species Apostichopus japonicus. We identified 1,862 phosphorylation sites in 1,169 proteins, and 712 acetylation sites in 470 proteins. Of the 147 and 251 proteins differentially modified by phosphorylation and acetylation, respectively, most were related to cytoskeleton biogenesis, protein synthesis and modification, signal recognition and transduction, energy production and conversion, or substance transport and metabolism. Phosphorylation appears to play a more important role in signal recognition and transduction than acetylation, while acetylation is of greater importance in posttranslational modification, protein turnover, chaperones; energy production and conversion; amino acid and lipid transport and metabolism. These results expanded our understanding of the regulatory mechanisms of posttranslational modifications in intestine regeneration of sea cucumbers after evisceration.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chenggang Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoni Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingchun Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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26
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Kraev A. Insertional Mutagenesis Confounds the Mechanism of the Morbid Phenotype of a PLN R9C Transgenic Mouse Line. J Card Fail 2018; 24:115-125. [PMID: 29325795 DOI: 10.1016/j.cardfail.2017.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND A mouse line with heterozygous transgenic expression of phospholamban carrying a substitution of cysteine for arginine 9 (TgPLNR9C) under the control of α-myosin heavy chain (αMHC) promoter features dilated cardiomyopathy, heart failure, and premature death. METHODS AND RESULTS Determination of transgene chromosomal localization by conventional methods shows that in this line the transgenic array of 13 PLNR9C expression cassettes, arranged in a head-to-tail tandem orientation, have integrated into the bidirectional promoter of the αMHC (Myh6) gene and the gene for the regulatory noncoding RNA Myheart (Mhrt), both of which are known to be involved in cardiac development and pathology. Expression of the noncoding RNA Mhrt in TgPLNR9C mice exhibits profound deregulation, despite the presence of the second, intact allele. CONCLUSIONS The TgPLNR9C mouse strain is, in the best case, a functionally ambiguous phenocopy of the human PLNR9C heterozygote, because a similar constellation of genetically programmed events can not occur in a patient. Publications featuring "cardiac-specific overexpression" are focused on the phenotype and typically forgo the definition of the transgene integration site or transgene temporal expression profile, so caution should be exercised in attributing clinical relevance to pathologic phenomena observed in αMHC-driven transgenes.
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Affiliation(s)
- Alexander Kraev
- University of Toronto, 27 King's College Circle, Toronto, Ontario M5S 1A1, Canada.
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27
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Xie J, Dong W, Liu R, Wang Y, Li Y. Research on the hepatotoxicity mechanism of citrate-modified silver nanoparticles based on metabolomics and proteomics. Nanotoxicology 2017; 12:18-31. [DOI: 10.1080/17435390.2017.1415389] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jiabin Xie
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Wenying Dong
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Rui Liu
- School of Chinese Materia Medica, Shanxi University of Traditional Chinese Medicine, Shanxi, PR China
| | - Yuming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
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28
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Ehsan M, Jiang H, L Thomson K, Gehmlich K. When signalling goes wrong: pathogenic variants in structural and signalling proteins causing cardiomyopathies. J Muscle Res Cell Motil 2017; 38:303-316. [PMID: 29119312 PMCID: PMC5742121 DOI: 10.1007/s10974-017-9487-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022]
Abstract
Cardiomyopathies are a diverse group of cardiac disorders with distinct phenotypes, depending on the proteins and pathways affected. A substantial proportion of cardiomyopathies are inherited and those will be the focus of this review article. With the wide application of high-throughput sequencing in the practice of clinical genetics, the roles of novel genes in cardiomyopathies are recognised. Here, we focus on a subgroup of cardiomyopathy genes [TTN, FHL1, CSRP3, FLNC and PLN, coding for Titin, Four and a Half LIM domain 1, Muscle LIM Protein, Filamin C and Phospholamban, respectively], which, despite their diverse biological functions, all have important signalling functions in the heart, suggesting that disturbances in signalling networks can contribute to cardiomyopathies.
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Affiliation(s)
- Mehroz Ehsan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - He Jiang
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Kate L Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Katja Gehmlich
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and British Heart Foundation Centre of Research Excellence, University of Oxford, Oxford, UK.
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29
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Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO. Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice. J Proteome Res 2017. [PMID: 28641008 DOI: 10.1021/acs.jproteome.7b00144] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cardiac fibroblasts (CFs) represent a major subpopulation of cells in the developing and adult heart. Cardiomyocyte (CM) and CF intercellular communication occurs through paracrine interactions and modulate myocyte development and stress response. Detailed proteomic analysis of the CF secretome in normal and stressed conditions may offer insights into the role of CF in heart development and disease. Primary neonatal mouse CFs were isolated and cultured for 24 h in 21% (normoxic) or 2% (hypoxic) O2. Conditioned medium was separated to obtain exosomes (EXO) and EXO-depleted secretome fractions. Multidimensional protein identification technology was performed on secreted fractions. Whole cell lysate data were also generated to provide subcellular context to the secretome. Proteomic analysis identified 6163 unique proteins in total. Statistical (QSpec) analysis identified 494 proteins differentially expressed between fractions and oxygen conditions. Gene Ontology enrichment analysis revealed hypoxic conditions selectively increase expression of proteins with extracellular matrix and signaling annotations. Finally, we subjected CM pretreated with CF secreted factors to hypoxia/reoxygenation. Viability assays suggested altered viability due to CF-derived factors. CF secretome proteomics revealed differential expression based on mode of secretion and oxygen levels in vitro.
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Affiliation(s)
- Jake Cosme
- Department of Physiology and Translational Biology and Engineering Program (TBEP), University of Toronto , Toronto, Ontario M5G 1M1, Canada
| | - Hongbo Guo
- The Donnelly Centre for Cellular and Biomolecular Research, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, Ontario M5S 3E1, Canada
| | - Sina Hadipour-Lakmehsari
- Department of Physiology and Translational Biology and Engineering Program (TBEP), University of Toronto , Toronto, Ontario M5G 1M1, Canada
| | - Andrew Emili
- The Donnelly Centre for Cellular and Biomolecular Research, Ted Rogers Centre for Heart Research, University of Toronto , Toronto, Ontario M5S 3E1, Canada
| | - Anthony O Gramolini
- Department of Physiology and Translational Biology and Engineering Program (TBEP), University of Toronto , Toronto, Ontario M5G 1M1, Canada
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30
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Dewan S, McCabe KJ, Regnier M, McCulloch AD. Insights and Challenges of Multi-Scale Modeling of Sarcomere Mechanics in cTn and Tm DCM Mutants-Genotype to Cellular Phenotype. Front Physiol 2017; 8:151. [PMID: 28352236 PMCID: PMC5348544 DOI: 10.3389/fphys.2017.00151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/24/2017] [Indexed: 01/18/2023] Open
Abstract
Dilated Cardiomyopathy (DCM) is a leading cause of sudden cardiac death characterized by impaired pump function and dilatation of cardiac ventricles. In this review we discuss various in silico approaches to elucidating the mechanisms of genetic mutations leading to DCM. The approaches covered in this review focus on bridging the spatial and temporal gaps that exist between molecular and cellular processes. Mutations in sarcomeric regulatory thin filament proteins such as the troponin complex (cTn) and Tropomyosin (Tm) have been associated with DCM. Despite the experimentally-observed myofilament measures of contractility in the case of these mutations, the mechanisms by which the underlying molecular changes and protein interactions scale up to organ failure by these mutations remains elusive. The review highlights multi-scale modeling approaches and their applicability to study the effects of sarcomeric gene mutations in-silico. We discuss some of the insights that can be gained from computational models of cardiac biomechanics when scaling from molecular states to cellular level.
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Affiliation(s)
- Sukriti Dewan
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kimberly J McCabe
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael Regnier
- Departments of Bioengineering and Medicine, University of Washington Seattle, WA, USA
| | - Andrew D McCulloch
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
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