Cardiac Proteome Profiling in Ischemic and Dilated Cardiomyopathy Mouse Models
28
Citation
56
Reference
10
Related Paper
Citation Trend
Abstract:
Heart failure is a worldwide pandemic with an unacceptable high level of morbidity and mortality. Understanding the different pathophysiological mechanisms will contribute to prevention and individualized therapy of heart failure. We established mouse models for ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM) by inducing myocardial infarction and Coxsackievirus B3 infection respectively. Isobaric tags for relative and absolute quantitation and liquid chromatography coupled with tandem mass spectrometry technology was used to identify the protein expression profiles in control and failing hearts. A total of 1638 proteins were identified and compared in this proteomics analysis. Among them, 286 proteins were differently expressed. Gene ontology, KEGG pathway and ingenuity pathway analysis was performed to systematically assess the potential connections of the differentially expressed proteins to biological functions. Compared with control group, the differentially expressed proteins derived from the hearts of ICM and DCM mice were partially similar and mainly modulated in oxidative phosphorylation, metabolism and protein folding pathways. Moreover, difference still existed, the differentially expressed proteins between DCM and ICM hearts were significantly modulated in oxidative phosphorylation, metabolic and AMPK signaling pathways. Confirmatory western bolt analysis demonstrated that SDHB was down-regulated in both ICM and DCM hearts, while UQCRQ, GLUT4 and adiponectin were up-regulated in ICM hearts. ATP concentration significantly decreased in both DCM and ICM hearts. The protein expression of phospho-AMPKα decreased significantly in DCM hearts, but increased in ICM. In summary, oxidative phosphorylation, cardiac metabolism and protein folding play critical roles in the pathogenesis of heart failure. The diverse changes in protein expression profiles between failing hearts induced by either myocardial infarction or CVB3 infection demonstrated the heterogeneity of heart failure. Understanding the differences in proteome profiles could offer more precise therapeutic options for heart failure.Keywords:
Dilated Cardiomyopathy
Proteome
KEGG
Ischemic Cardiomyopathy
Blood serum samples are the major source for clinical proteomics approaches, which aim to identify diagnostically relevant or treatment-response related proteins. But, the presence of very high-abundance proteins and the enormous dynamic range of protein distribution hinders whole serum analysis. An innovative tool to overcome these limitations, utilizes combinatorial hexapeptide ligand libraries (ProteoMiner). Here, we demonstrate that ProteoMiner can be used for comparative and quantitative analysis of complex proteomes. We spiked serum samples with increasing amounts (3 microg to 300 microg) of whole E. coli lysate, processed it with ProteoMiner and performed quantitative analyses of 2D-gels. We found, that the concentration of the spiked bacteria proteome, reflected by the maintained proportional spot intensities, was not altered by ProteoMiner treatment. Therefore, we conclude that the ProteoMiner technology can be used for quantitative analysis of low abundant proteins in complex biological samples.
Proteome
Quantitative Analysis
Cite
Citations (62)
Quantitative proteomics involves the identification and quantitation of protein components in various biological systems. Stable isotope labelling technology, by both metabolic and chemical methods, has been the most commonly used approach for global proteome-wide profiling. Recently, its capability has been extended from labelled pairs to multiple labels, allowing for the simultaneous quantification of multiplex samples. The ion intensity-based quantitative approach has progressively gained more popularity as mass spectrometry performance has improved significantly. Although some success has been reported, it remains difficult comprehensively to characterise the global proteome, due to its enormous complexity and dynamic range. The use of sub-proteome fractionation techniques permits a simplification of the proteome and provides a practical step towards the ultimate dissection of the entire proteome. Further development of the technology for targeting sub-proteomes on a functional basis — such as selecting proteins with differential expression profiles from mass spectrometric analyses, for further mass spectrometric sequencing in an intelligent manner — is expected in the near future.
Proteome
Multiplex
Profiling (computer programming)
Cite
Citations (119)
Proteome
Cite
Citations (24)
Abstract Stable isotope labelling in combination with mass spectrometry has emerged as a powerful tool to identify and relatively quantify thousands of proteins within complex protein mixtures. Here we describe a novel method, termed isotope‐coded protein label (ICPL), which is capable of high‐throughput quantitative proteome profiling on a global scale. Since ICPL is based on stable isotope tagging at the frequent free amino groups of isolated intact proteins, it is applicable to any protein sample, including extracts from tissues or body fluids, and compatible to all separation methods currently employed in proteome studies. The method showed highly accurate and reproducible quantification of proteins and yielded high sequence coverage, indispensable for the detection of post‐translational modifications and protein isoforms. The efficiency ( e.g. accuracy, dynamic range, sensitivity, speed) of the approach is demonstrated by comparative analysis of two differentially spiked proteomes.
Proteome
Cite
Citations (516)
Abstract Background The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences. Results KEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally. Conclusions KEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.
KEGG
Metabolic pathway
Cite
Citations (155)
Proteome
Tandem mass tag
Isobaric labeling
Human proteome project
Cite
Citations (79)
Abstract Dilated Cardiomyopathy is a high-incident disease, which diagnosis of and treatments are clinical priority. The aim of our study was to evaluate the diagnostic potential of cardiac magnetic resonance (CMR) imaging; echocardiography and the biochemical parameters that can help us differentiate between the post-ischemic and non-ischemic dilated cardiomyopathy. Materials and methods. The study enrolled 134 patients with dilated cardiomyopathy: 74 with the post-ischemic form and 60 with the non-ischemic one. All patients underwent a coronary imaging test, with echocardiogram, cardiac magnetic resonance and a blood test. Pro-inflammatory cytokines were evaluated using Luminex kit. Data was compared between the two groups. Results. Echocardiography allowed recognition of Left Ventricular Non Compaction in 2 patients. Longitudinal and circumferential strains were significantly different in the two groups (p<0.05). Using CMR imaging a post-myocarditis scar was diagnosed in 2 patients and a post-ischemic scar in 95% of patients with the chronic ischemic disease. The interleukin IL-1, IL-6 and TNF-α levels were higher in the post-ischemic group compared with the non-ischemic one. Conclusions. The use of second level techniques with a high sensitivity and specificity would help distinguish among different sub-forms of dilated cardiomyopathy.
Dilated Cardiomyopathy
Ischemic Cardiomyopathy
Cite
Citations (9)
Dilated Cardiomyopathy
Ischemic Cardiomyopathy
Cite
Citations (0)
Quantitative proteomics is an essential tool in proteome research since it enables measuring changes in protein abundance in response to biological perturbations. During the last few years, different quantitative strategies have been developed in proteomics to compare different experimental conditions, including label-free and isobaric chemical labeling approaches. Here we show that different quantitation techniques have an important influence on detected sample variability, and we use the combination of six different quantitation strategies to perform a proteome comparison of three different Mycoplasma pneumoniae strains (ldh knockdown, Δprkc, and wild-type). The integration of the different datasets indicates that the ldh knockdown strongly affects the abundance of ribosomal proteins and enzymes involved in the regulation of the cellular redox state, whereas the prkc deletion affects key cellular physiological processes such as protein and DNA synthesis, and cytoadherence.
Proteome
Ribosomal protein
Isobaric labeling
Cite
Citations (0)
As mass-spectrometry-based quantitative proteomics approaches become increasingly powerful, researchers are taking advantage of well established methodologies and improving instrumentation to pioneer new protein expression profiling methods. For example, pooling several proteomes labeled using the stable isotope labeling by amino acids in cell culture (SILAC) method yields a whole-proteome stable isotope-labeled internal standard that can be mixed with a tissue-derived proteome for quantification. By increasing quantitative accuracy in the analysis of tissue proteomes, such methods should improve integration of protein expression profiling data with transcriptomic data and enhance downstream bioinformatic analyses. An accurate and scalable quantitative method to analyze tumor proteomes at the depth of several thousand proteins provides a powerful tool for global protein quantification of tissue samples and promises to redefine our understanding of tumor biology.
Proteome
Label-free Quantification
Isobaric labeling
Cite
Citations (15)