Characterization of Zebrafish Cardiac Proteome Using Online pH Gradient SCX–RP HPLC–MS/MS Platform

Zhang, Jiang; Lanham, Kevin A.; Heideman, Warren; Peterson, Richard E.

doi:10.1007/978-1-62703-386-2_10

Cited by 6 publications

(5 citation statements)

References 15 publications

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“…Despite their small size, which makes tissue procurement challenging, these models are being increasingly utilized for proteomics studies (e.g. MS) , including the cardiac proteome .…”

Section: Human Heart Failurementioning

confidence: 99%

Sizing up models of heart failure: Proteomics from flies to humans

Kooij

Venkatraman

Tra

et al. 2014

Proteomics Clinical Apps

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Cardiovascular disease is the leading cause of death in the western world. Heart failure is a heterogeneous and complex syndrome, arising from various etiologies, which result in cellular phenotypes that vary from patient to patient. The ability to utilize genetic manipulation and biochemical experimentation in animal models has made them indispensable in the study of this chronic condition. Similarly, proteomics has been helpful for elucidating complicated cellular and molecular phenotypes and has the potential to identify circulating biomarkers and drug targets for therapeutic intervention. In this review, the use of human samples and animal model systems (pig, dog, rat, mouse, zebrafish, and fruit fly) in cardiac research is discussed. Additionally, the protein sequence homology between these species and the extent of conservation at the level of the phospho-proteome in major kinase signaling cascades involved in heart failure are investigated.

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“…Despite their small size, which makes tissue procurement challenging, these models are being increasingly utilized for proteomics studies (e.g. MS) , including the cardiac proteome .…”

Section: Human Heart Failurementioning

confidence: 99%

Sizing up models of heart failure: Proteomics from flies to humans

Kooij

Venkatraman

Tra

et al. 2014

Proteomics Clinical Apps

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“…Despite tremendous amounts of genomics and transcriptomics datasets, corresponding information on cardiac proteomes and their differences across models is still scarce [28]. Previous proteomics studies of model organisms have illuminated portions of their cardiac proteomes [29,30], often with a particular focus such as cardiac development [31], disease models [32], subcellular protein expression [33,34], phosphorylation [35][36][37], protein turnover [12,38], or smaller mammals and amphibians [16]. The deepest human heart dataset obtained to date presents an impressive atlas [39], but it cannot be utilized for quantitative comparisons as it was acquired from tissue collected several days postmortem [14].…”

Section: Discussionmentioning

confidence: 99%

Quantitative proteome comparison of human hearts with those of model organisms

et al. 2021

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Delineating human cardiac pathologies and their basic molecular mechanisms relies on research conducted in model organisms. Yet translating findings from preclinical models to humans present a significant challenge, in part due to differences in cardiac protein expression between humans and model organisms. Proteins immediately determine cellular function, yet their large-scale investigation in hearts has lagged behind those of genes and transcripts. Here, we set out to bridge this knowledge gap: By analyzing protein profiles in humans and commonly used model organisms across cardiac chambers, we determine their commonalities and regional differences. We analyzed cardiac tissue from each chamber of human, pig, horse, rat, mouse, and zebrafish in biological replicates. Using mass spectrometry–based proteomics workflows, we measured and evaluated the abundance of approximately 7,000 proteins in each species. The resulting knowledgebase of cardiac protein signatures is accessible through an online database: atlas.cardiacproteomics.com. Our combined analysis allows for quantitative evaluation of protein abundances across cardiac chambers, as well as comparisons of cardiac protein profiles across model organisms. Up to a quarter of proteins with differential abundances between atria and ventricles showed opposite chamber-specific enrichment between species; these included numerous proteins implicated in cardiac disease. The generated proteomics resource facilitates translational prospects of cardiac studies from model organisms to humans by comparisons of disease-linked protein networks across species.

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“…Specifically, we present a quantitative high-resolution map of cardiac protein expression across humans and five common model organisms. Previous studies of model organisms have illuminated portions of their cardiac proteomes 10,19,20 , but often with a particular focus such as cardiac development 21 , disease models 22 , subcellular protein expression 23,24 , phosphorylation [25][26][27] , protein turnover 8,28 or focused on smaller mammals and amphibians 16 or human tissue collected several days post-mortem 29 . No study has been presented that allowed for direct comparison of cardiac protein profiles between model organisms and human.…”

Section: Discussionmentioning

confidence: 99%

Proteomics Dissection of Cardiac Protein Profiles of Humans and Model Organisms

Linscheid

Santos

Poulsen

et al. 2020

Preprint

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The study of human cardiac pathologies often relies on research conducted in model organisms to gain molecular insight into disease and to develop novel treatment strategies; however, translating findings from model organisms back to human can present a significant challenge, in part due to a lack of knowledge about the differences across species in cardiac protein abundances and their interactions. Here we set out to bridge this knowledge gap by presenting a global analysis of cardiac protein expression profiles in humans and commonly used model organisms. Using quantitative mass spectrometry-based proteomics, we measured the abundance of ~7,000 proteins in samples from the separate chambers of human, pig, horse, rat, mouse and zebrafish hearts. This knowledgebase of cardiac protein signatures is accessible through an online database at: atlas.cardiacproteomics.com. Quantitative comparison of the protein profiles support the pig as model organism of choice for arrhythmogenic right ventricular cardiomyopathy whereas comparison of profiles from the two-chambered zebrafish heart suggests a better resemblance to the right side of mammalian hearts. This proteomics resource

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Characterization of Zebrafish Cardiac Proteome Using Online pH Gradient SCX–RP HPLC–MS/MS Platform

Cited by 6 publications

References 15 publications

Sizing up models of heart failure: Proteomics from flies to humans

Sizing up models of heart failure: Proteomics from flies to humans

Quantitative proteome comparison of human hearts with those of model organisms

Proteomics Dissection of Cardiac Protein Profiles of Humans and Model Organisms

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