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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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Karpurapu A, Williams HA, DeBenedittis P, Baker CE, Ren S, Thomas MC, Beard AJ, Devlin GW, Harrington J, Parker LE, Smith AK, Mainsah B, Pla MM, Asokan A, Bowles DE, Iversen E, Collins L, Karra R. Deep Learning Resolves Myovascular Dynamics in the Failing Human Heart. JACC Basic Transl Sci 2024; 9:674-686. [PMID: 38984052 PMCID: PMC11228115 DOI: 10.1016/j.jacbts.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 07/11/2024]
Abstract
The adult mammalian heart harbors minute levels of cycling cardiomyocytes (CMs). Large numbers of images are needed to accurately quantify cycling events using microscopy-based methods. CardioCount is a new deep learning-based pipeline to rigorously score nuclei in microscopic images. When applied to a repository of 368,434 human microscopic images, we found evidence of coupled growth between CMs and cardiac endothelial cells in the adult human heart. Additionally, we found that vascular rarefaction and CM hypertrophy are interrelated in end-stage heart failure. CardioCount is available for use via GitHub and via Google Colab for users with minimal machine learning experience.
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Affiliation(s)
- Anish Karpurapu
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Helen A. Williams
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Paige DeBenedittis
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Caroline E. Baker
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Simiao Ren
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, USA
| | - Michael C. Thomas
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Anneka J. Beard
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Garth W. Devlin
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Josephine Harrington
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Lauren E. Parker
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Abigail K. Smith
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Boyla Mainsah
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, USA
| | - Michelle Mendiola Pla
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Aravind Asokan
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Dawn E. Bowles
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Edwin Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Leslie Collins
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, USA
| | - Ravi Karra
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
- Duke Regeneration Center, Durham, North Carolina, USA
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3
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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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4
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Santos‐Ferreira D, Diaz SO, Ferreira JP, Girerd N, Pellicori P, Mariottoni B, Cosmi F, Hazebroek M, Verdonschot JA, Cuthbert J, Petutschnigg J, Heymans S, Staessen JA, Pieske B, Edelmann F, Clark AL, Rossignol P, Fontes‐Carvalho R, Cleland JG, Zannad F. Phenotyping patients with ischaemic heart disease at risk of developing heart failure: an analysis of the HOMAGE trial. ESC Heart Fail 2024; 11:209-218. [PMID: 37939716 PMCID: PMC10804163 DOI: 10.1002/ehf2.14465] [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: 02/16/2023] [Revised: 05/15/2023] [Accepted: 06/21/2023] [Indexed: 11/10/2023] Open
Abstract
AIMS We aim to characterize the clinical and proteomic profiles of patients at risk of developing heart failure (HF), with and without coronary artery disease (CAD) or prior myocardial infarction (MI). METHODS AND RESULTS HOMAGE evaluated the effect of spironolactone on plasma and serum markers of fibrosis over 9 months of follow-up in participants with (or at risk of having) CAD, and raised natriuretic peptides. In this post hoc analysis, patients were classified as (i) neither CAD nor MI; (ii) CAD; or (iii) MI. Proteomic between-group differences were evaluated through logistic regression and narrowed using backward stepwise selection and bootstrapping. Among the 527 participants, 28% had neither CAD or MI, 31% had CAD, and 41% had prior MI. Compared with people with neither CAD nor MI, those with CAD had higher baseline plasma concentrations of matrix metalloproteinase-7 (MMP-7), galectin-4 (GAL4), plasminogen activator inhibitor 1 (PAI-1), and lower plasma peptidoglycan recognition protein 1 (PGLYRP1), whilst those with a history of MI had higher plasma MMP-7, neurotrophin-3 (NT3), pulmonary surfactant-associated protein D (PSPD), and lower plasma tumour necrosis factor-related activation-induced cytokine (TRANCE). Proteomic signatures were similar for patients with CAD or prior MI. Treatment with spironolactone was associated with an increase of MMP7, NT3, and PGLYRP1 at 9 months. CONCLUSIONS In patients at risk of developing HF, those with CAD or MI had a different proteomic profile regarding inflammatory, immunological, and collagen catabolic processes.
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Affiliation(s)
- Diogo Santos‐Ferreira
- Department of CardiologyCentro Hospitalar Vila Nova de Gaia/EspinhoVila Nova de GaiaPortugal
- Department of Surgery and Physiology, Cardiovascular R&D Centre ‐ UnIC@RISEFaculty of Medicine of the University of PortoPortoPortugal
| | - Sílvia O. Diaz
- Department of Surgery and Physiology, Cardiovascular R&D Centre ‐ UnIC@RISEFaculty of Medicine of the University of PortoPortoPortugal
| | - João Pedro Ferreira
- Department of Surgery and Physiology, Cardiovascular R&D Centre ‐ UnIC@RISEFaculty of Medicine of the University of PortoPortoPortugal
- Inserm, Centre d'Investigation Clinique Plurithématique 1433, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
| | - Nicolas Girerd
- Inserm, Centre d'Investigation Clinique Plurithématique 1433, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
| | | | | | - Franco Cosmi
- Inserm, Centre d'Investigation Clinique Plurithématique 1433, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
| | - Mark Hazebroek
- Department of CardiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Job A.J. Verdonschot
- Department of CardiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Joe Cuthbert
- Department of CardiologyUniversity of Hull, Castle Hill HospitalCottinghamUK
| | - Johannes Petutschnigg
- Department of Internal Medicine and CardiologyCharité University Medicine, Berlin Institute of Health (BIH), and German Centre for Cardiovascular Research (DZHK), Partner Site BerlinBerlinGermany
| | - Stephane Heymans
- Department of CardiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jan A. Staessen
- Non‐Profit Research Association Alliance for the Promotion of Preventive Medicine (APPREMED)MechelenBelgium
| | - Burkert Pieske
- Department of Internal Medicine and CardiologyCharité University Medicine, Berlin Institute of Health (BIH), and German Centre for Cardiovascular Research (DZHK), Partner Site BerlinBerlinGermany
- German Heart Center BerlinBerlinGermany
| | - Frank Edelmann
- Department of Internal Medicine and CardiologyCharité University Medicine, Berlin Institute of Health (BIH), and German Centre for Cardiovascular Research (DZHK), Partner Site BerlinBerlinGermany
| | - Andrew L. Clark
- Department of CardiologyUniversity of Hull, Castle Hill HospitalCottinghamUK
| | - Patrick Rossignol
- Inserm, Centre d'Investigation Clinique Plurithématique 1433, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
| | - Ricardo Fontes‐Carvalho
- Department of CardiologyCentro Hospitalar Vila Nova de Gaia/EspinhoVila Nova de GaiaPortugal
- Department of Surgery and Physiology, Cardiovascular R&D Centre ‐ UnIC@RISEFaculty of Medicine of the University of PortoPortoPortugal
| | - John G.F. Cleland
- School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUK
| | - Faiez Zannad
- Inserm, Centre d'Investigation Clinique Plurithématique 1433, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
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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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6
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Wang J, Zhu X, Wang S, Zhang Y, Hua W, Liu Z, Zheng Y, Lu X. Phosphoproteomic and proteomic profiling in post-infarction chronic heart failure. Front Pharmacol 2023; 14:1181622. [PMID: 37405054 PMCID: PMC10315476 DOI: 10.3389/fphar.2023.1181622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Background: Post-infarction chronic heart failure is the most common type of heart failure. Patients with chronic heart failure show elevated morbidity and mortality with limited evidence-based therapies. Phosphoproteomic and proteomic analysis can provide insights regarding molecular mechanisms underlying post-infarction chronic heart failure and explore new therapeutic approaches. Methods and results: Global quantitative phosphoproteomic and proteomic analysis of left ventricular tissues from post-infarction chronic heart failure rats were performed. A total of 33 differentially expressed phosphorylated proteins (DPPs) and 129 differentially expressed proteins were identified. Bioinformatic analysis indicated that DPPs were enriched mostly in nucleocytoplasmic transport and mRNA surveillance pathway. Bclaf1 Ser658 was identified after construction of Protein-Protein Interaction Network and intersection with Thanatos Apoptosis Database. Predicted Upstream Kinases of DPPs based on kinase-substrate enrichment analysis (KSEA) app showed 13 kinases enhanced in heart failure. Proteomic analysis showed marked changes in protein expression related to cardiac contractility and metabolism. Conclusion: The present study marked phosphoproteomics and proteomics changes in post-infarction chronic heart failure. Bclaf1 Ser658 might play a critical role in apoptosis in heart failure. PRKAA1, PRKACA, and PAK1 might serve as potential therapeutic targets for post-infarction chronic heart failure.
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Affiliation(s)
| | | | | | | | | | | | - Yu Zheng
- *Correspondence: Yu Zheng, ; Xiao Lu,
| | - Xiao Lu
- *Correspondence: Yu Zheng, ; Xiao Lu,
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7
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Reitz C, Tavassoli M, Kim D, Shah S, Lakin R, Teng A, Zhou YQ, Li W, Hadipour-Lakmehsari S, Backx P, Emili A, Oudit G, Kuzmanov U, Gramolini A. Proteomics and phosphoproteomics of failing human left ventricle identifies dilated cardiomyopathy-associated phosphorylation of CTNNA3. Proc Natl Acad Sci U S A 2023; 120:e2212118120. [PMID: 37126683 PMCID: PMC10175742 DOI: 10.1073/pnas.2212118120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023] Open
Abstract
The prognosis and treatment outcomes of heart failure (HF) patients rely heavily on disease etiology, yet the majority of underlying signaling mechanisms are complex and not fully elucidated. Phosphorylation is a major point of protein regulation with rapid and profound effects on the function and activity of protein networks. Currently, there is a lack of comprehensive proteomic and phosphoproteomic studies examining cardiac tissue from HF patients with either dilated dilated cardiomyopathy (DCM) or ischemic cardiomyopathy (ICM). Here, we used a combined proteomic and phosphoproteomic approach to identify and quantify more than 5,000 total proteins with greater than 13,000 corresponding phosphorylation sites across explanted left ventricle (LV) tissue samples, including HF patients with DCM vs. nonfailing controls (NFC), and left ventricular infarct vs. noninfarct, and periinfarct vs. noninfarct regions of HF patients with ICM. Each pair-wise comparison revealed unique global proteomic and phosphoproteomic profiles with both shared and etiology-specific perturbations. With this approach, we identified a DCM-associated hyperphosphorylation cluster in the cardiomyocyte intercalated disc (ICD) protein, αT-catenin (CTNNA3). We demonstrate using both ex vivo isolated cardiomyocytes and in vivo using an AAV9-mediated overexpression mouse model, that CTNNA3 phosphorylation at these residues plays a key role in maintaining protein localization at the cardiomyocyte ICD to regulate conductance and cell-cell adhesion. Collectively, this integrative proteomic/phosphoproteomic approach identifies region- and etiology-associated signaling pathways in human HF and describes a role for CTNNA3 phosphorylation in the pathophysiology of DCM.
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Affiliation(s)
- Cristine J. Reitz
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Marjan Tavassoli
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Da Hye Kim
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Saumya Shah
- Department of Medicine, University of Alberta, Edmonton, ABT6G 2R3
| | - Robert Lakin
- Department of Biology, York University, Toronto, ONM3J 1P3
| | - Allen C. T. Teng
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Yu-Qing Zhou
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Wenping Li
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Sina Hadipour-Lakmehsari
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Peter H. Backx
- Department of Biology, York University, Toronto, ONM3J 1P3
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, MA02118
- Department of Biology, Boston University School of Medicine, Boston, MA02118
- The Centre for Network Systems Biology, Boston University School of Medicine, Boston, MA02118
| | - Gavin Y. Oudit
- Department of Medicine, University of Alberta, Edmonton, ABT6G 2R3
- Mazankowski Alberta Heart Institute, Edmonton, ABT6G 2B7
| | - Uros Kuzmanov
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
| | - Anthony O. Gramolini
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ONM5S 1M8
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ONM5G 1M1
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8
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Drakos SG, Badolia R, Makaju A, Kyriakopoulos CP, Wever-Pinzon O, Tracy CM, Bakhtina A, Bia R, Parnell T, Taleb I, Ramadurai DKA, Navankasattusas S, Dranow E, Hanff TC, Tseliou E, Shankar TS, Visker J, Hamouche R, Stauder EL, Caine WT, Alharethi R, Selzman CH, Franklin S. Distinct Transcriptomic and Proteomic Profile Specifies Patients Who Have Heart Failure With Potential of Myocardial Recovery on Mechanical Unloading and Circulatory Support. Circulation 2023; 147:409-424. [PMID: 36448446 PMCID: PMC10062458 DOI: 10.1161/circulationaha.121.056600] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Extensive evidence from single-center studies indicates that a subset of patients with chronic advanced heart failure (HF) undergoing left ventricular assist device (LVAD) support show significantly improved heart function and reverse structural remodeling (ie, termed "responders"). Furthermore, we recently published a multicenter prospective study, RESTAGE-HF (Remission from Stage D Heart Failure), demonstrating that LVAD support combined with standard HF medications induced remarkable cardiac structural and functional improvement, leading to high rates of LVAD weaning and excellent long-term outcomes. This intriguing phenomenon provides great translational and clinical promise, although the underlying molecular mechanisms driving this recovery are largely unknown. METHODS To identify changes in signaling pathways operative in the normal and failing human heart and to molecularly characterize patients who respond favorably to LVAD unloading, we performed global RNA sequencing and phosphopeptide profiling of left ventricular tissue from 93 patients with HF undergoing LVAD implantation (25 responders and 68 nonresponders) and 12 nonfailing donor hearts. Patients were prospectively monitored through echocardiography to characterize their myocardial structure and function and identify responders and nonresponders. RESULTS These analyses identified 1341 transcripts and 288 phosphopeptides that are differentially regulated in cardiac tissue from nonfailing control samples and patients with HF. In addition, these unbiased molecular profiles identified a unique signature of 29 transcripts and 93 phosphopeptides in patients with HF that distinguished responders after LVAD unloading. Further analyses of these macromolecules highlighted differential regulation in 2 key pathways: cell cycle regulation and extracellular matrix/focal adhesions. CONCLUSIONS This is the first study to characterize changes in the nonfailing and failing human heart by integrating multiple -omics platforms to identify molecular indices defining patients capable of myocardial recovery. These findings may guide patient selection for advanced HF therapies and identify new HF therapeutic targets.
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Affiliation(s)
- Stavros G. Drakos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Rachit Badolia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Aman Makaju
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Christos P. Kyriakopoulos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Omar Wever-Pinzon
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Christopher M. Tracy
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Anna Bakhtina
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Ryan Bia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Timothy Parnell
- Bioinformatics Core, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States
| | - Iosif Taleb
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Dinesh K. A. Ramadurai
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Sutip Navankasattusas
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth Dranow
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thomas C. Hanff
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Eleni Tseliou
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thirupura S. Shankar
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Joseph Visker
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Rana Hamouche
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth L. Stauder
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - William T. Caine
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Rami Alharethi
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Craig H. Selzman
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
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9
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Sharma P, Beck D, Murtha LA, Figtree G, Boyle A, Gentile C. Fibulin-3 Deficiency Protects Against Myocardial Injury Following Ischaemia/ Reperfusion in in vitro Cardiac Spheroids. Front Cardiovasc Med 2022; 9:913156. [PMID: 35795376 PMCID: PMC9251181 DOI: 10.3389/fcvm.2022.913156] [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: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 12/02/2022] Open
Abstract
Myocardial infarction (MI, or heart attack) is a leading cause of death worldwide. Myocardial ischaemia reperfusion (I/R) injury typical of MI events is also associated with the development of cardiac fibrosis and heart failure in patients. Fibulin-3 is an extracellular matrix component that plays a role in regulating MI response in the heart. In this study, we generated and compared in vitro cardiac spheroids (CSs) from wild type (WT) and fibulin-3 knockout (Fib-3 KO) mice. These were then exposed to pathophysiological changes in oxygen (O2) concentrations to mimic an MI event. We finally measured changes in contractile function, cell death, and mRNA expression levels of cardiovascular disease genes between WT and Fib-3 KO CSs. Our results demonstrated that there are significant differences in growth kinetics and endothelial network formation between WT and Fib-3 KO CSs, however, they respond similarly to changes in O2 concentrations. Fib-3 deficiency resulted in an increase in viability of cells and improvement in contraction frequency and fractional shortening compared to WT I/R CSs. Gene expression analyses demonstrated that Fib-3 deficiency inhibits I/R injury and cardiac fibrosis and promotes angiogenesis in CSs. Altogether, our findings suggest that Fib-3 deficiency makes CSs resistant to I/R injury and associated cardiac fibrosis and helps to improve the vascular network in CSs.
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Affiliation(s)
- Poonam Sharma
- College of Health Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
- Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
- Faculty of Medicine and Health, Northern Clinical School, The University of Sydney, Sydney, NSW, Australia
- Faculty of Engineering and IT, School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Dominik Beck
- Faculty of Engineering and IT, School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Lucy A. Murtha
- College of Health Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
| | - Gemma Figtree
- Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
- Faculty of Medicine and Health, Northern Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Andrew Boyle
- College of Health Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia
| | - Carmine Gentile
- Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
- Faculty of Medicine and Health, Northern Clinical School, The University of Sydney, Sydney, NSW, Australia
- Faculty of Engineering and IT, School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
- *Correspondence: Carmine Gentile
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10
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Pathologic Proteolytic Processing of N-Cadherin as a Marker of Human Fibrotic Disease. Cells 2022; 11:cells11010156. [PMID: 35011717 PMCID: PMC8750447 DOI: 10.3390/cells11010156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/27/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023] Open
Abstract
Prior research has implicated the involvement of cell adhesion molecule N-cadherin in tissue fibrosis and remodeling. We hypothesize that anomalies in N-cadherin protein processing are involved in pathological fibrosis. Diseased tissues associated with fibrosis of the heart, lung, and liver were probed for the precursor form of N-cadherin, pro-N-cadherin (PNC), by immunohistochemistry and compared to healthy tissues. Myofibroblast cell lines were analyzed for cell surface pro-N-cadherin by flow cytometry and immunofluorescent microscopy. Soluble PNC products were immunoprecipitated from patient plasmas and an enzyme-linked immunoassay was developed for quantification. All fibrotic tissues examined show aberrant PNC localization. Cell surface PNC is expressed in myofibroblast cell lines isolated from cardiomyopathy and idiopathic pulmonary fibrosis but not on myofibroblasts isolated from healthy tissues. PNC is elevated in the plasma of patients with cardiomyopathy (p ≤ 0.0001), idiopathic pulmonary fibrosis (p ≤ 0.05), and nonalcoholic fatty liver disease with cirrhosis (p ≤ 0.05). Finally, we have humanized a murine antibody and demonstrate that it significantly inhibits migration of PNC expressing myofibroblasts. Collectively, the aberrant localization of PNC is observed in all fibrotic tissues examined in our study and our data suggest a role for cell surface PNC in the pathogenesis of fibrosis.
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11
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Markandran K, Yu H, Song W, Lam DTUH, Madathummal MC, Ferenczi MA. Functional and Molecular Characterisation of Heart Failure Progression in Mice and the Role of Myosin Regulatory Light Chains in the Recovery of Cardiac Muscle Function. Int J Mol Sci 2021; 23:ijms23010088. [PMID: 35008512 PMCID: PMC8745055 DOI: 10.3390/ijms23010088] [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] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023] Open
Abstract
Heart failure (HF) as a result of myocardial infarction (MI) is a major cause of fatality worldwide. However, the cause of cardiac dysfunction succeeding MI has not been elucidated at a sarcomeric level. Thus, studying the alterations within the sarcomere is necessary to gain insights on the fundamental mechansims leading to HF and potentially uncover appropriate therapeutic targets. Since existing research portrays regulatory light chains (RLC) to be mediators of cardiac muscle contraction in both human and animal models, its role was further explored In this study, a detailed characterisation of the physiological changes (i.e., isometric force, calcium sensitivity and sarcomeric protein phosphorylation) was assessed in an MI mouse model, between 2D (2 days) and 28D post-MI, and the changes were related to the phosphorylation status of RLCs. MI mouse models were created via complete ligation of left anterior descending (LAD) coronary artery. Left ventricular (LV) papillary muscles were isolated and permeabilised for isometric force and Ca2+ sensitivity measurement, while the LV myocardium was used to assay sarcomeric proteins’ (RLC, troponin I (TnI) and myosin binding protein-C (MyBP-C)) phosphorylation levels and enzyme (myosin light chain kinase (MLCK), zipper interacting protein kinase (ZIPK) and myosin phosphatase target subunit 2 (MYPT2)) expression levels. Finally, the potential for improving the contractility of diseased cardiac papillary fibres via the enhancement of RLC phosphorylation levels was investigated by employing RLC exchange methods, in vitro. RLC phosphorylation and isometric force potentiation were enhanced in the compensatory phase and decreased in the decompensatory phase of HF failure progression, respectively. There was no significant time-lag between the changes in RLC phosphorylation and isometric force during HF progression, suggesting that changes in RLC phosphorylation immediately affect force generation. Additionally, the in vitro increase in RLC phosphorylation levels in 14D post-MI muscle segments (decompensatory stage) enhanced its force of isometric contraction, substantiating its potential in HF treatment. Longitudinal observation unveils potential mechanisms involving MyBP-C and key enzymes regulating RLC phosphorylation, such as MLCK and MYPT2 (subunit of MLCP), during HF progression. This study primarily demonstrates that RLC phosphorylation is a key sarcomeric protein modification modulating cardiac function. This substantiates the possibility of using RLCs and their associated enzymes to treat HF.
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Affiliation(s)
- Kasturi Markandran
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
| | - Haiyang Yu
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
| | - Weihua Song
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
| | - Do Thuy Uyen Ha Lam
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore
| | - Mufeeda Changaramvally Madathummal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
- A*STAR Microscopy Platform—Electron Microscopy, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Michael A. Ferenczi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore; (K.M.); (H.Y.); (W.S.); (D.T.U.H.L.); (M.C.M.)
- Brunel Medical School, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
- Correspondence:
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12
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Chunhacha P, Pinkaew D, Sinthujaroen P, Bowles DE, Fujise K. Fortilin inhibits p53, halts cardiomyocyte apoptosis, and protects the heart against heart failure. Cell Death Discov 2021; 7:310. [PMID: 34689154 PMCID: PMC8542040 DOI: 10.1038/s41420-021-00692-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023] Open
Abstract
Heart failure (HF) has reached epidemic proportions in developed countries, affecting over 20 million people worldwide. Despite modern medical and device therapies, 60–70% of HF patients still die within 5 years of diagnosis as it relentlessly progresses through pervasive apoptotic loss of cardiomyocytes. Although fortilin, a 172-amino-acid anti-p53 molecule, is one of the most expressed proteins in the heart, its precise role there has remained unknown. Also unclear is how cardiomyocytes are protected against apoptosis. Here, we report that failing human hearts express less fortilin than do non-failing hearts. We also found that mice lacking fortilin in the heart (fortilinKO-heart) die by 9 weeks of age due to extensive cardiomyocyte apoptosis and severe HF, which suggests that fortilin sustains cardiomyocyte viability. The lack of fortilin is also associated with drastic upregulation of p53 target genes in the hearts. The heart-specific deletion of p53 in fortilinKO-heart mice extends their life spans from 9 to 18 weeks by mitigating cardiomyocyte apoptosis. Our data suggest that fortilin is a novel cardiac p53 inhibitor and that its inadequate expression in failing hearts and subsequent overactivation of the p53 apoptosis pathway in cardiomyocytes exacerbates HF.
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Affiliation(s)
- Preedakorn Chunhacha
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.,Department of Biochemistry and Microbiology, and Cell-based Drug and Health Product Development Research Unit (CDD), Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Decha Pinkaew
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Patuma Sinthujaroen
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.,Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Dawn E Bowles
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham, NC, 27710, USA
| | - Ken Fujise
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, 98109, USA.
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13
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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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14
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Safabakhsh S, Panwar P, Barichello S, Sangha SS, Hanson PJ, Van Petegem F, Laksman Z. THE ROLE OF PHOSPHORYLATION IN ATRIAL FIBRILLATION: A FOCUS ON MASS SPECTROMETRY APPROACHES. Cardiovasc Res 2021; 118:1205-1217. [PMID: 33744917 DOI: 10.1093/cvr/cvab095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/16/2021] [Indexed: 11/14/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia worldwide. It is associated with significant increases in morbidity in the form of stroke and heart failure, and a doubling in all-cause mortality. The pathophysiology of AF is incompletely understood, and this has contributed to a lack of effective treatments and disease-modifying therapies. An important cellular process that may explain how risk factors give rise to AF includes post-translational modification (PTM) of proteins. As the most commonly occurring PTM, protein phosphorylation is especially relevant. Although many methods exist for studying protein phosphorylation, a common and highly resolute technique is mass spectrometry (MS). This review will discuss recent evidence surrounding the role of protein phosphorylation in the pathogenesis of AF. MS-based technology to study phosphorylation and uses of MS in other areas of medicine such as oncology will also be presented. Based on these data, future goals and experiments will be outlined that utilize MS technology to better understand the role of phosphorylation in AF and elucidate its role in AF pathophysiology. This may ultimately allow for the development of more effective AF therapies.
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Affiliation(s)
- Sina Safabakhsh
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pankaj Panwar
- AbCellera Biologicals Inc., Vancouver, British Columbia, Canada
| | - Scott Barichello
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarabjit S Sangha
- Cellular and Regenerative Medicine Centre, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, British Columbia, Canada.,Molecular Cardiac Physiology Group, Departments of Biomedical Physiology and Kinesiology and Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada
| | - Paul J Hanson
- UBC Heart Lung Innovation Centre, Vancouver, British Columbia, Canada.,UBC Department of Pathology and Laboratory Medicine, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary Laksman
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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15
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A systematic review of post-translational modifications in the mitochondrial permeability transition pore complex associated with cardiac diseases. Biochim Biophys Acta Mol Basis Dis 2020; 1867:165992. [PMID: 33091565 DOI: 10.1016/j.bbadis.2020.165992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/23/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022]
Abstract
The mitochondrial permeability transition pore (mPTP) opening is involved in the pathophysiology of multiple cardiac diseases, such as ischemia/reperfusion injury and heart failure. A growing number of evidence provided by proteomic screening techniques has demonstrated the role of post-translational modifications (PTMs) in several key components of the pore in response to changes in the extra/intracellular environment and bioenergetic demand. This could lead to a fine, complex regulatory mechanism that, under pathological conditions, can shift the state of mitochondrial functions and, thus, the cell's fate. Understanding the complex relationship between these PTMs is still under investigation and can provide new, promising therapeutic targets and treatment approaches. This review, using a systematic review of the literature, presents the current knowledge on PTMs of the mPTP and their role in health and cardiac disease.
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16
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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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17
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Wang X, Shen X, Weil BR, Young RF, Canty JM, Qu J. Quantitative proteomic and phosphoproteomic profiling of ischemic myocardial stunning in swine. Am J Physiol Heart Circ Physiol 2020; 318:H1256-H1271. [PMID: 32223553 DOI: 10.1152/ajpheart.00713.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite decades of research on the pathophysiology of myocardial stunning, protein changes and/or phosphorylation status underlying alterations in cardiac function/structure remain inadequately understood. Here, we utilized comprehensive and quantitative proteomic and phosphoproteomic approaches to explore molecular mechanisms of myocardial stunning in swine. The closed-chest swine (n = 5 pigs) were subjected to a 10-min left anterior descending coronary artery (LAD) occlusion producing regional myocardial stunning. Tissues from the ischemic LAD region and a remote nonischemic area of the left ventricle were collected 1 h after reperfusion. Ion current-based proteomics (IonStar) and quantitative phosphoproteomics were employed in parallel to identify alterations in protein level and site-specific phosphorylation changes. A novel swine heart protein database exhibiting high accuracy and low redundancy was developed here to facilitate comprehensive study. Further informatic investigations identified potential protein-protein interactions in stunned myocardium. In total, we quantified 2,099 protein groups and 4,699 phosphorylation sites with only 0.4% missing values. Proteomic analyses revealed downregulation of contractile function and extracellular matrix remodeling. Meanwhile, alterations in phosphorylation linked with contractile dysfunction and apoptotic cell death were uncovered. NetworKIN/STRING analysis predicted regulatory kinases responsible for altered phosphosites, such as protein kinase C-mediated phosphorylation of cardiac troponin I-S199 and CaMKII-mediated phosphorylation of phospholamban-T17. In summary, the ion current-based proteomics and phosphoproteomics reliably identified novel alterations in protein content and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium, which corroborate well with our physiological observations. Moreover, this work developed a comprehensive database of the swine heart proteome, a highly valuable resource for future translational research in porcine models with cardiovascular diseases.NEW & NOTEWORTHY We first used ion current-based proteomics and phosphoproteomics to reliably identify novel alterations in protein expression and phosphorylation contributing to contractile dysfunction, extracellular matrix (ECM) damage, and programmed cell death in stunned myocardium and developed a comprehensive swine heart-specific proteome database, which provides a valuable resource for future research in porcine models of cardiovascular diseases.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York
| | - Xiaomeng Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Brian R Weil
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York
| | - Rebeccah F Young
- Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - John M Canty
- Department of Physiology and Biophysics, University at Buffalo, Buffalo, New York.,Veterans Affairs Western New York Healthcare System, Buffalo, New York.,Clinical and Translational Research Center, University at Buffalo, Buffalo, New York.,Division of Cardiovascular Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jun Qu
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.,New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York.,Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York
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18
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Singh R, Liyanage R, Gupta C, Lay JO, Pereira A, Rojas CM. The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes. FRONTIERS IN PLANT SCIENCE 2020; 11:232. [PMID: 32194606 PMCID: PMC7064621 DOI: 10.3389/fpls.2020.00232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
AtNHR2A (Arabidopsis thaliana nonhost resistance 2A) and AtNHR2B (Arabidopsis thaliana nonhost resistance 2B) are two proteins that participate in nonhost resistance, a broad-spectrum mechanism of plant immunity that protects plants against the majority of potential pathogens. AtNHR2A and AtNHR2B are localized to the cytoplasm, chloroplasts, and other subcellular compartments of unknown identity. The multiple localizations of AtNHR2A and AtNHR2B suggest that these two proteins are highly dynamic and versatile, likely participating in multiple biological processes. In spite of their importance, the specific functions of AtNHR2A and AtNHR2B have not been elucidated. Thus, to aid in the functional characterization of these two proteins and identify the biological processes in which these proteins operate, we used immunoprecipitation coupled with mass spectrometry (IP-MS) to identify proteins interacting with AtNHR2A and AtNHR2B and to generate their interactome network. Further validation of three of the identified proteins provided new insights into specific pathways and processes related to plant immunity where AtNHR2A and AtNHR2B participate. Moreover, the comprehensive analysis of the AtNHR2A- and AtNHR2B-interacting proteins using published empirical information revealed that the functions of AtNHR2A and AtNHR2B are not limited to plant immunity but encompass other biological processes.
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Affiliation(s)
- Raksha Singh
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Purdue University, West Lafayette, IN, United States
| | - Rohana Liyanage
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chirag Gupta
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Jackson O. Lay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Clemencia M. Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
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19
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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20
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Beak JY, Kang HS, Huang W, Myers PH, Bowles DE, Jetten AM, Jensen BC. The nuclear receptor RORα protects against angiotensin II-induced cardiac hypertrophy and heart failure. Am J Physiol Heart Circ Physiol 2019; 316:H186-H200. [PMID: 30387679 PMCID: PMC6383360 DOI: 10.1152/ajpheart.00531.2018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/04/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023]
Abstract
The nuclear receptor retinoic acid-related orphan receptor-α (RORα) regulates numerous critical biological processes, including central nervous system development, lymphocyte differentiation, and lipid metabolism. RORα has been recently identified in the heart, but very little is known about its role in cardiac physiology. We sought to determine whether RORα regulates myocardial hypertrophy and cardiomyocyte survival in the context of angiotensin II (ANG II) stimulation. For in vivo characterization of the function of RORα in the context of pathological cardiac hypertrophy and heart failure, we used the "staggerer" (RORαsg/sg) mouse, which harbors a germline mutation encoding a truncated and globally nonfunctional RORα. RORαsg/sg and wild-type littermate mice were infused with ANG II or vehicle for 14 days. For in vitro experiments, we overexpressed or silenced RORα in neonatal rat ventricular myocytes (NRVMs) and human cardiac fibroblasts exposed to ANG II. RORαsg/sg mice developed exaggerated myocardial hypertrophy and contractile dysfunction after ANG II treatment. In vitro gain- and loss-of-function experiments were consistent with the discovery that RORα inhibits ANG II-induced pathological hypertrophy and cardiomyocyte death in vivo. RORα directly repressed IL-6 transcription. Loss of RORα function led to enhanced IL-6 expression, proinflammatory STAT3 activation (phopho-STAT3 Tyr705), and decreased mitochondrial number and function, oxidative stress, hypertrophy, and death of cardiomyocytes upon ANG II exposure. RORα was less abundant in failing compared with nonfailing human heart tissue. In conclusion, RORα protects against ANG II-mediated pathological hypertrophy and heart failure by suppressing the IL-6-STAT3 pathway and enhancing mitochondrial function. NEW & NOTEWORTHY Mice lacking retinoic acid-related orphan receptor-α (RORα) develop exaggerated cardiac hypertrophy after angiotensin II infusion. Loss of RORα leads to enhanced IL-6 expression and NF-κB nuclear translocation. RORα maintains mitochondrial function and reduces oxidative stress after angiotensin II. The abundance of RORα is reduced in failing mouse and human hearts.
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MESH Headings
- Angiotensin II/toxicity
- Animals
- Cardiomegaly/etiology
- Cardiomegaly/genetics
- Cardiomegaly/metabolism
- Cells, Cultured
- Female
- Fibroblasts/drug effects
- Fibroblasts/metabolism
- Heart Failure/etiology
- Heart Failure/genetics
- Heart Failure/metabolism
- Humans
- Interleukin-6/metabolism
- Loss of Function Mutation
- Mice
- Mice, Inbred C57BL
- Middle Aged
- Mitochondria, Heart/metabolism
- Myocardial Contraction
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/physiology
- Nuclear Receptor Subfamily 1, Group F, Member 1/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism
- Rats
- Rats, Sprague-Dawley
- STAT3 Transcription Factor/metabolism
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Affiliation(s)
- Ju Youn Beak
- McAllister Heart Institute University of North Carolina School of Medicine , Chapel Hill, North Carolina
| | - Hong Soon Kang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , Research Triangle Park, North Carolina
| | - Wei Huang
- McAllister Heart Institute University of North Carolina School of Medicine , Chapel Hill, North Carolina
| | - Page H Myers
- Veterinary Medicine Section, Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health , Research Triangle Park, North Carolina
| | - Dawn E Bowles
- Department of Surgery, Duke University Medical Center , Durham, North Carolina
| | - Anton M Jetten
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health , Research Triangle Park, North Carolina
| | - Brian C Jensen
- McAllister Heart Institute University of North Carolina School of Medicine , Chapel Hill, North Carolina
- Division of Cardiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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21
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Ledee D, Kang MA, Kajimoto M, Purvine S, Brewer H, Pasa-Tolic L, Portman MA. Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model. Am J Physiol Heart Circ Physiol 2017; 313:H125-H137. [PMID: 28455290 PMCID: PMC5538860 DOI: 10.1152/ajpheart.00842.2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 01/26/2023]
Abstract
Ischemia-reperfusion (I/R) results in altered metabolic and molecular responses, and phosphorylation is one of the most noted regulatory mechanisms mediating signaling mechanisms during physiological stresses. To expand our knowledge of the potential phosphoproteomic changes in the myocardium during I/R, we used Isobaric Tags for Relative and Absolute Quantitation-based analyses in left ventricular samples obtained from porcine hearts under control or I/R conditions. The data are available via ProteomeXchange with identifier PXD006066. We identified 1,896 phosphopeptides within left ventricular control and I/R porcine samples. Significant differential phosphorylation between control and I/R groups was discovered in 111 phosphopeptides from 86 proteins. Analysis of the phosphopeptides using Motif-x identified five motifs: (..R..S..), (..SP..), (..S.S..), (..S…S..), and (..S.T..). Semiquantitative immunoblots confirmed site location and directional changes in phosphorylation for phospholamban and pyruvate dehydrogenase E1, two proteins known to be altered by I/R and identified by this study. Novel phosphorylation sites associated with I/R were also identified. Functional characterization of the phosphopeptides identified by our methodology could expand our understanding of the signaling mechanisms involved during I/R damage in the heart as well as identify new areas to target therapeutic strategies.NEW & NOTEWORTHY We used Isobaric Tags for Relative and Absolute Quantitation technology to investigate the phosphoproteomic changes that occur in cardiac tissue under ischemia-reperfusion conditions. The results of this study provide an extensive catalog of phosphoproteins, both predicted and novel, associated with ischemia-reperfusion, thereby identifying new pathways for investigation.
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Affiliation(s)
- Dolena Ledee
- Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
- Division of Cardiology, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Min A Kang
- Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
| | - Masaki Kajimoto
- Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington
| | - Samuel Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington; and
| | - Heather Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington; and
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington; and
| | - Michael A Portman
- Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, Washington;
- Division of Cardiology, Department of Pediatrics, University of Washington, Seattle, Washington
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22
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Foster MW, Gwinn WM, Kelly FL, Brass DM, Valente AM, Moseley MA, Thompson JW, Morgan DL, Palmer SM. Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl. J Proteome Res 2017; 16:538-549. [PMID: 27966365 DOI: 10.1021/acs.jproteome.6b00672] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Occupational exposures to the diketone flavoring agent, diacetyl, have been associated with bronchiolitis obliterans, a rare condition of airway fibrosis. Model studies in rodents have suggested that the airway epithelium is a major site of diacetyl toxicity, but the effects of diacetyl exposure upon the human airway epithelium are poorly characterized. Here we performed quantitative LC-MS/MS-based proteomics to study the effects of repeated diacetyl vapor exposures on 3D organotypic cultures of human primary tracheobronchial epithelial cells. Using a label-free approach, we quantified approximately 3400 proteins and 5700 phosphopeptides in cell lysates across four independent donors. Altered expression of proteins and phosphopeptides were suggestive of loss of cilia and increased squamous differentiation in diacetyl-exposed cells. These phenomena were confirmed by immunofluorescence staining of culture cross sections. Hyperphosphorylation and cross-linking of basal cell keratins were also observed in diacetyl-treated cells, and we used parallel reaction monitoring to confidently localize and quantify previously uncharacterized sites of phosphorylation in keratin 6. Collectively, these data identify numerous molecular changes in the epithelium that may be important to the pathogenesis of flavoring-induced bronchiolitis obliterans. More generally, this study highlights the utility of quantitative proteomics for the study of in vitro models of airway injury and disease.
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Affiliation(s)
| | - William M Gwinn
- National Institute of Environmental Health Sciences , Research Triangle Park, North Carolina 27709, United States
| | | | | | | | | | | | - Daniel L Morgan
- National Institute of Environmental Health Sciences , Research Triangle Park, North Carolina 27709, United States
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23
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Lam MPY, Ping P, Murphy E. Proteomics Research in Cardiovascular Medicine and Biomarker Discovery. J Am Coll Cardiol 2016; 68:2819-2830. [PMID: 28007144 PMCID: PMC5189682 DOI: 10.1016/j.jacc.2016.10.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/21/2022]
Abstract
Proteomics is a systems physiology discipline to address the large-scale characterization of protein species within a biological system, be it a cell, a tissue, a body biofluid, an organism, or a cohort population. Building on advances from chemical analytical platforms (e.g., mass spectrometry and other technologies), proteomics approaches have contributed powerful applications in cardiovascular biomedicine, most notably in: 1) the discovery of circulating protein biomarkers of heart diseases from plasma samples; and 2) the identification of disease mechanisms and potential therapeutic targets in cardiovascular tissues, in both preclinical models and translational studies. Contemporary proteomics investigations offer powerful means to simultaneously examine tens of thousands of proteins in various samples, and understand their molecular phenotypes in health and disease. This concise review introduces study design considerations, example applications and use cases, as well as interpretation and analysis of proteomics data in cardiovascular biomedicine.
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Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California.
| | - Peipei Ping
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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24
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Cabiati M, Svezia B, Matteucci M, Botta L, Pucci A, Rinaldi M, Caselli C, Lionetti V, Del Ry S. Myocardial Expression Analysis of Osteopontin and Its Splice Variants in Patients Affected by End-Stage Idiopathic or Ischemic Dilated Cardiomyopathy. PLoS One 2016; 11:e0160110. [PMID: 27479215 PMCID: PMC4968805 DOI: 10.1371/journal.pone.0160110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/13/2016] [Indexed: 02/02/2023] Open
Abstract
Osteopontin (OPN) is a phosphoglycoprotein of cardiac extracellular matrix and it is still poorly defined whether its expression changes in failing heart of different origin. The full-length OPN-a and its isoforms (OPN-b, OPN-c) transcriptomic profile were evaluated in myocardium of patients with dilated or ischemic cardiomyopathy (DCM n = 8; LVEF% = 17.5±3; ICM n = 8; LVEF% = 19.5±5.2) and in auricle of valvular patients (VLP n = 5; LVEF%≥50), by Real-time PCR analysis. OPN-a and thrombin mRNA levels resulted significantly higher in DCM compared to ICM patients (DCM:31.3±7.4, ICM:2.7±1.1, p = 0.0002; DCM:19.1±4.9, ICM:5.4±2.2, p = 0.007, respectively). Although both genes’ mRNA levels increased in patients with LVEF<50% (DCM+ICM) with respect to VLP with LVEF>50%, a significant increase in OPN (p = 0.0004) and thrombin (p = 0.001) expression was observed only in DCM. In addition, a correlation between OPN-a and thrombin was found in patients with LVEF<50% (r = 0.6; p = 0.003). The mRNA pattern was confirmed by OPN-a cardiac protein concentration (VLP:1.127±0.26; DCM:1.29±0.22; ICM:1.00±0.077 ng/ml). The OPN splice variants expression were detectable only in ICM (OPN-b: 0.357±0.273; OPN-c: 0.091±0.033) and not in DCM patients. A significant correlation was observed between collagen type I, evaluated by immunohistochemistry analysis, and both OPN-a mRNA expression (r = 0.87, p = 0.002) and OPN protein concentrations (r = 0.77, p = 0.016). Concluding, OPN-a and thrombin mRNA resulted dependent on the origin of heart failure while OPN-b and OPN-c highlighted a different expression for DCM and ICM patients, suggesting their correlation with different clinical-pathophysiological setting.
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Affiliation(s)
| | - Benedetta Svezia
- CNR Institute of Clinical Physiology, Pisa, Italy
- Laboratory of Translational Critical Care Medicine, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Marco Matteucci
- Laboratory of Translational Critical Care Medicine, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Luca Botta
- Department of cardiac Surgery, Niguarda Ca’ Granda Hospital, Milan, Italy
| | - Angela Pucci
- Department of Pathology, University Hospital Pisa, Pisa, Italy
| | - Mauro Rinaldi
- Cardiac Surgery Department, Cardiothoracic Department, A.O.U. Città della Salute e della Scienza di Torino, Presidio Molinette, and University of Torino, Turin, Italy
| | | | - Vincenzo Lionetti
- Laboratory of Translational Critical Care Medicine, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- * E-mail: (SDR); (VL)
| | - Silvia Del Ry
- CNR Institute of Clinical Physiology, Pisa, Italy
- * E-mail: (SDR); (VL)
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25
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Gross SM, Lehman SL. Functional phosphorylation sites in cardiac myofilament proteins are evolutionarily conserved in skeletal myofilament proteins. Physiol Genomics 2016; 48:377-87. [PMID: 26993364 DOI: 10.1152/physiolgenomics.00112.2015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/11/2016] [Indexed: 01/14/2023] Open
Abstract
Protein phosphorylation plays an important role in regulating cardiac contractile function, but phosphorylation is not thought to play a regulatory role in skeletal muscle. To examine how myofilament phosphorylation arose in the human heart, we analyzed the amino acid sequences of 25 cardiac phosphorylation sites in animals ranging from fruit flies to humans. These analyses indicated that of the 25 human phosphorylation sites examined, 11 have been conserved across vertebrates and four have been sporadically present in vertebrates. Furthermore, all 11 of the cardiac sites found across vertebrates were present in skeletal muscle isoforms, along with three sites that were sporadically present. Based on the conservation of amino acid sequences between cardiac and skeletal contractile proteins, we tested for phosphorylation in mammalian skeletal muscle using several biochemical techniques and found evidence that multiple myofilament proteins were phosphorylated. Several of these phosphorylation sites were validated using mass spectrometry, including one site that is present in slow- and fast-twitch troponin I (TnI), but was lost in cardiac TnI. Thus, several myofilament phosphorylation sites present in the human heart likely arose in invertebrate muscle, have been evolutionarily conserved in skeletal muscle, and potentially have functional effects in both skeletal and cardiac muscle.
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Affiliation(s)
- Sean M Gross
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California; and Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon
| | - Steven L Lehman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California; and
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26
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Lindoso RS, Sandim V, Collino F, Carvalho AB, Dias J, da Costa MR, Zingali RB, Vieyra A. Proteomics of cell-cell interactions in health and disease. Proteomics 2015; 16:328-44. [PMID: 26552723 DOI: 10.1002/pmic.201500341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
The mechanisms of cell-cell communications are now under intense study by proteomic approaches. Proteomics has unraveled changes in protein profiling as the result of cell interactions mediated by ligand/receptor, hormones, soluble factors, and the content of extracellular vesicles. Besides being a brief overview of the main and profitable methodologies now available (evaluating theory behind the methods, their usefulness, and pitfalls), this review focuses on-from a proteome perspective-some signaling pathways and post-translational modifications (PTMs), which are essential for understanding ischemic lesions and their recovery in two vital organs in mammals, the heart, and the kidney. Knowledge of misdirection of the proteome during tissue recovery, such as represented by the convergence between fibrosis and cancer, emerges as an important tool in prognosis. Proteomics of cell-cell interaction is also especially useful for understanding how stem cells interact in injured tissues, anticipating clues for rational therapeutic interventions. In the effervescent field of induced pluripotency and cell reprogramming, proteomic studies have shown what proteins from specialized cells contribute to the recovery of infarcted tissues. Overall, we conclude that proteomics is at the forefront in helping us to understand the mechanisms that underpin prevalent pathological processes.
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Affiliation(s)
- Rafael S Lindoso
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Vanessa Sandim
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Federica Collino
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, Turin, Italy.,Translational Center of Regenerative Medicine, University of Turin/Fresenius Medical Care, Turin, Italy
| | - Adriana B Carvalho
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil
| | - Juliana Dias
- National Institute of Cancer, Rio de Janeiro, RJ, Brazil
| | - Milene R da Costa
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Russolina B Zingali
- National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Proteomic Network of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,National Institute of Science and Technology for Structural Biology and Bioimaging, Rio de Janeiro, RJ, Brazil.,Translational Biomedicine Graduate Program, Grand Rio University, Duque de Caxias, RJ, Brazil
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27
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Schindler RFR, Scotton C, Zhang J, Passarelli C, Ortiz-Bonnin B, Simrick S, Schwerte T, Poon KL, Fang M, Rinné S, Froese A, Nikolaev VO, Grunert C, Müller T, Tasca G, Sarathchandra P, Drago F, Dallapiccola B, Rapezzi C, Arbustini E, Di Raimo FR, Neri M, Selvatici R, Gualandi F, Fattori F, Pietrangelo A, Li W, Jiang H, Xu X, Bertini E, Decher N, Wang J, Brand T, Ferlini A. POPDC1(S201F) causes muscular dystrophy and arrhythmia by affecting protein trafficking. J Clin Invest 2015; 126:239-53. [PMID: 26642364 DOI: 10.1172/jci79562] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 10/29/2015] [Indexed: 01/16/2023] Open
Abstract
The Popeye domain-containing 1 (POPDC1) gene encodes a plasma membrane-localized cAMP-binding protein that is abundantly expressed in striated muscle. In animal models, POPDC1 is an essential regulator of structure and function of cardiac and skeletal muscle; however, POPDC1 mutations have not been associated with human cardiac and muscular diseases. Here, we have described a homozygous missense variant (c.602C>T, p.S201F) in POPDC1, identified by whole-exome sequencing, in a family of 4 with cardiac arrhythmia and limb-girdle muscular dystrophy (LGMD). This allele was absent in known databases and segregated with the pathological phenotype in this family. We did not find the allele in a further screen of 104 patients with a similar phenotype, suggesting this mutation to be family specific. Compared with WT protein, POPDC1(S201F) displayed a 50% reduction in cAMP affinity, and in skeletal muscle from patients, both POPDC1(S201F) and WT POPDC2 displayed impaired membrane trafficking. Forced expression of POPDC1(S201F) in a murine cardiac muscle cell line (HL-1) increased hyperpolarization and upstroke velocity of the action potential. In zebrafish, expression of the homologous mutation (popdc1(S191F)) caused heart and skeletal muscle phenotypes that resembled those observed in patients. Our study therefore identifies POPDC1 as a disease gene causing a very rare autosomal recessive cardiac arrhythmia and LGMD, expanding the genetic causes of this heterogeneous group of inherited rare diseases.
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28
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New Insights in the Diagnosis and Treatment of Heart Failure. BIOMED RESEARCH INTERNATIONAL 2015; 2015:265260. [PMID: 26634204 PMCID: PMC4637457 DOI: 10.1155/2015/265260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/21/2015] [Indexed: 12/22/2022]
Abstract
Cardiovascular disease is the leading cause of mortality in the US and in westernized countries with ischemic heart disease accounting for the majority of these deaths. Paradoxically, the improvements in the medical and surgical treatments of acute coronary syndrome are leading to an increasing number of “survivors” who are then developing heart failure. Despite considerable advances in its management, the gold standard for the treatment of end-stage heart failure patients remains heart transplantation. Nevertheless, this procedure can be offered only to a small percentage of patients who could benefit from a new heart due to the limited availability of donor organs. The aim of this review is to evaluate the safety and efficacy of innovative approaches in the diagnosis and treatment of patients refractory to standard medical therapy and excluded from cardiac transplantation lists.
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29
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Abstract
Heart failure in children is a complex clinical syndrome with multiple aetiologies. The underlying disorders that lead to heart failure in children differ significantly from those in adults. Some clinical biomarkers for heart failure status and prognosis appear to be useful in both age groups. This review outlines the use and the present status of biomarkers for heart failure in paediatric cardiology. Furthermore, clinical scenarios in which development of new biomarkers might address management or prognosis are discussed. Finally, strategies for proteomic discovery of novel biomarkers and application to practice are described.
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