Studying heart disease using the proteomic approach

Proteomics of the heart

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.

OMICS approaches in cardiovascular diseases: a mini review

Ranked in the topmost position among the deadliest diseases in the world, cardiovascular diseases (CVDs) are a global burden with alterations in heart and blood vessels. Early diagnostics and prognostics could be the best possible solution in CVD management. OMICS (genomics, proteomics, transcriptomics, and metabolomics) approaches could be able to tackle the challenges against CVDs. Genome-wide association studies along with next-generation sequencing with various computational biology tools could lead a new sight in early detection and possible therapeutics of CVDs. Human cardiac proteins are also characterized by mass spectrophotometry which could open the scope of proteomics approaches in CVD. Besides this, regulation of gene expression by transcriptomics approaches exhibits a new insight while metabolomics is the endpoint on the downstream of multi-omics approaches to confront CVDs from the early onset. Although a lot of challenges needed to overcome in CVD management, OMICS approaches are certainly a new prospect.

Isobaric tags for relative and absolute quantification-based proteomic analysis of defense responses triggered by the fungal pathogen Fusarium graminearum in wheat

Fusarium head blight (FHB) is a devastating disease worldwide that is predominantly caused by the fungal pathogen Fusarium graminearum. The aim of this work was to study differentially abundant protein species of near-isogenic lines A061-3 and A061-4 with the final goal of elucidating the molecular mechanisms of their differential resistance to F. graminearum. The objectives were accomplished using isobaric tags for relative and absolute quantification (iTRAQ) with mass spectrometry (MS). Lines A061-3 and A061-4 were resistant and susceptible to F. graminearum, respectively. At four post-inoculation points, 11,070 protein species were identified, of which 762 were differentially abundant. Gene Ontology enrichment analysis showed that most differentially abundant protein species participated in 18 biological processes after inoculation. Further analysis demonstrated that crucial metabolic pathways like plant-pathogen interaction had increased abundance. Real-time quantitative PCR (qRT-PCR) analysis revealed increased gene products of eight selected genes in plant-pathogen interaction. This investigation provides a basic bioinformatics-based characterization of differentially abundant protein species during early stages against F. graminearum. SIGNIFICANCE: FHB leads to severe yield loss and reduction in grain quality in wheat and other small grain cereals. Although extensive studies have focused on wheat resistance against F. graminearum, the molecular mechanism of FHB resistance in wheat remains to be further elucidated. In the present study, Kyoto Encyclopedia of Genes and Genomes analysis indicated that ten pathways were putatively associated with FHB resistance. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) showed that a valuable set of differentially abundant protein species including pathogenesis-related protein species were identified for further discovery of candidate genes for FHB resistance. This investigation provides new insights into the molecular mechanisms associated with FHB resistance and as well as a foundation for future studies.

Understanding Leishmania parasites through proteomics and implications for the clinic

INTRODUCTION

Leishmania spp. are causative agents of leishmaniasis, a broad-spectrum neglected vector-borne disease. Genomic and transcriptional studies are not capable of solving intricate biological mysteries, leading to the emergence of proteomics, which can provide insights into the field of parasite biology and its interactions with the host. Areas covered: The combination of genomics and informatics with high throughput proteomics may improve our understanding of parasite biology and pathogenesis. This review analyses the roles of diverse proteomic technologies that facilitate our understanding of global protein profiles and definition of parasite development, survival, virulence and drug resistance mechanisms for disease intervention. Additionally, recent innovations in proteomics have provided insights concerning the drawbacks associated with conventional chemotherapeutic approaches and Leishmania biology, host-parasite interactions and the development of new therapeutic approaches. Expert commentary: With progressive breakthroughs in the foreseeable future, proteome profiles could provide target molecules for vaccine development and therapeutic intervention. Furthermore, proteomics, in combination with genomics and informatics, could facilitate the elimination of several diseases. Taken together, this review provides an outlook on developments in Leishmania proteomics and their clinical implications.

iTRAQ-Based Proteomic Analysis Reveals Recovery of Impaired Mitochondrial Function in Ischemic Myocardium by Shenmai Formula

Shenmai formula (SM) has been a traditional medicinal remedy for treating cardiovascular diseases in China for 800 years; however, its mechanism of action remains unclear. To explore the mechanism underlying cardioprotective effects of SM, iTRAQ-based proteomic approach was applied to analyze protein of myocardium in rats with myocardial ischemic injury. Upon treatment with SM and its two major components Red ginseng (RG) and Radix Ophiopogonis (OP), 101 differentially expressed proteins were filtered from a total of 712 detected and annotated proteins. They can be classified according to their locations and functions, while most of them are located in intracellular organelle, participating in cellular metabolic process. The functions of them are mostly associated with mitochondrial oxidative phosphorylation/respiration. The differentially expressed proteins were validated by liquid chromatography-tandem mass spectrometry and Western blotting (ATP5D, NDUFB10, TNNC1). Further in vitro experiments found that SM could attenuate hypoxia induced impairment of mitochondrial membrane potential and cellular ATP concentration in neonatal rat ventricular myocytes. Interestingly, the result of quantitative mitochondrial biogenesis assays revealed that SM had dominant positive effects on the maximum respiration, ATP-coupled respiration, and spare capacity of mitochondria in response to hypoxia. Hence, our findings suggest that SM promotes mitochondrial function to protect cardiomyocytes against hypoxia, which provides a possible illustration for conventional botanical therapy on a molecular level.

Proteomic profiling implies mitochondrial dysfunction in tachycardia-induced heart failure

BACKGROUND/OBJECTIVES

Molecular mechanisms of congestive heart failure as reflected by alterations of protein expression patterns are still incompletely analyzed. We therefore investigated intraventricular (ie, left ventricular congestive heart failure [LV-CHF] vs. LV-control [CTRL], and right ventricular [RV]-CHF vs. RV-CTRL) and interventricular (ie, LV-CHF vs. RV-CHF, and LV-CTRL vs. RV-CTRL) protein expression differences in an animal model.

METHODS

The model of rapid ventricular pacing in rabbits was combined with a proteomic approach using 2-dimensional gel electrophoresis. Identification of proteins was done by matrix-assisted laser desorption/ionization-tandem mass spectrometry (MALDI-MS/MS).

RESULTS

Rapid ventricular pacing-induced heart failure was characterized by LV dilatation, dysfunction, and hypotension as well as by increased BNP gene expression. By comparing LV-CHF vs. LV-CTRL, proteins were found to be underexpressed at 3 crucial points of cellular energy metabolism. In RV-CHF vs. RV-CTRL, proteins belonging to respiratory chain complexes were underexpressed, but additionally a disturbance in the nitric oxide-generating enzymatic apparatus was seen. Regarding the interventricular analyses, a stronger expression of energetic pathways was accompanied by an underexpression of contractile and stress response proteins in failing left vs. right ventricles. Finally, significant protein expression differences were found in LV-CTRL vs. RV-CTRL reflecting a higher expression of contractile, stress response, and respiratory chain proteins in LV tissue.

CONCLUSIONS

In tachycardia-induced heart failure, significant inter- and intraventricular protein expression patterns were found with a predominance of proteins, which are involved in cellular energy metabolism.

Autoimmunoreactive IgGs from patients with postural orthostatic tachycardia syndrome

PURPOSE

Autoantibodies are implicated in the pathogenesis of cardiovascular diseases and cardiac arrhythmias. In this pilot study, we tested the hypothesis that autoantibodies are present in patients with postural orthostatic tachycardia syndrome (POTS).

EXPERIMENTAL DESIGN

Seven control subjects (6 F:1 M, average age 36.1 years) and ten patients with the diagnosis of POTS (7 F: 3 M, average age 35.1 years) provided informed consent and 30 mL of venous blood. Human heart membrane proteins were resolved by 2DE and immunoblotted against purified IgGs from controls and patients.

RESULTS

Eighteen protein spots immunoreactive specifically against patient IgGs were detected and they were excised from gels, trypsin-digested, and analyzed by nanoLC-electrospray MS/MS. Forty unique proteins were identified and these include proteins that are associated with cardiac hypertrophy (mimecan, myozenin), cardiac remodeling (periostin), cardiomyopathy (desmin, desmoplakin), cell survival (laminin), structural integrity (filamin), chaperone proteins (crystalline, HSP70), mitochondrial enzymes, and channel proteins. Ingenuity Pathway Analysis showed multiple pathways were involved including those that regulate energy metabolism, redox, fibrosis, cardiac hypertrophy, and degeneration.

CONCLUSIONS AND CLINICAL RELEVANCE

Autoantibodies are present in patients with POTS. These autoantibodies cross-react with a wide range of cardiac proteins and may induce alterations in cardiac function. Autoimmune pathogenetic mechanisms should be further explored in these patients.

Proteomics: a reality-check for putative stem cells

The concept of using stem cells for cardiovascular repair holds great potential, but uncertainties in preclinical experiments must be addressed before their therapeutic application. Contemporary proteomic techniques can help to characterize cell preparations more thoroughly and identify some of the potential causes that may lead to a high failure rate in clinical trials. The first part of this review discusses the broader application of proteomics to stem cell research by providing an overview of the main proteomic technologies and how they might help the translation of stem cell therapy. The second part focuses on the controversy about endothelial progenitor cells (EPCs) and raises cautionary flags for marker assignment and assessment of cell purity. A proteomics-led approach in early outgrowth EPCs has already raised the awareness that markers used to define their endothelial potential may arise from an uptake of platelet proteins. A platelet microparticle-related transfer of endothelial characteristics to mononuclear cells can result in a misinterpretation of the assay. The necessity to perform counterstaining for platelet markers in this setting is not fully appreciated. Similarly, the presence of platelets and platelet microparticles is not taken into consideration when functional improvements are directly attributed to EPCs, whereas saline solutions or plain medium serve as controls. Thus, proteomics shed new light on the caveats of a common stem cell assay in cardiovascular research, which might explain some of the inconsistencies in the field.

Studies of complex biological systems with applications to molecular medicine: the need to integrate transcriptomic and proteomic approaches

Omics approaches to the study of complex biological systems with potential applications to molecular medicine are attracting great interest in clinical as well as in basic biological research. Genomics, transcriptomics and proteomics are characterized by the lack of an a priori definition of scope, and this gives sufficient leeway for investigators (a) to discern all at once a globally altered pattern of gene/protein expression and (b) to examine the complex interactions that regulate entire biological processes. Two popular platforms in "omics" are DNA microarrays, which measure messenger RNA transcript levels, and proteomic analyses, which identify and quantify proteins. Because of their intrinsic strengths and weaknesses, no single approach can fully unravel the complexities of fundamental biological events. However, an appropriate combination of different tools could lead to integrative analyses that would furnish new insights not accessible through one-dimensional datasets. In this review, we will outline some of the challenges associated with integrative analyses relating to the changes in metabolic pathways that occur in complex pathophysiological conditions (viz. ageing and altered thyroid state) in relevant metabolically active tissues. In addition, we discuss several new applications of proteomic analysis to the investigation of mitochondrial activity.

Recent progress of proteomics in critical illness

Critical illness, such as sepsis or septic shock with multiple organ dysfunction syndrome, is the leading cause of morbidity and mortality in intensive care units. The complexity of critical illness requires a robust methodology to explore the underlying mechanisms. Proteomics represents a powerful postgenomic biotechnology used for simultaneous examination of a large number of proteins or the proteome. Recent progress in proteomic techniques allows thorough evaluation of molecular changes associated with critical illness, thereby permitting to identify novel biomarkers and therapeutic targets. This review provides an update on the recent progress and potential of rapidly evolving proteomics approach to facilitate new discoveries in the field of critical care medicine.

In vitro and in vivo examination of cardiac troponins as biochemical markers of drug-induced cardiotoxicity

Cardiac troponin T (cTnT) and troponin I (cTnI) are becoming acknowledged as useful biochemical markers of drug-induced cardiotoxicity. In this study we examined the release kinetics of cTnT and cTnI using an in vitro model of isolated rat neonatal ventricular cardiomyocytes (NVCM, 72h treatment with 0.1-3microM of daunorubicin) and compared it with data from a rabbit model of chronic anthracycline-induced cardiomyopathy in vivo (3mg/kg of daunorubicin weekly, 10 weeks). In cell-culture media, the cTnI and cTnT concentrations were concentration- and time-dependently increasing in response to daunorubicin exposure and were negatively exponentially related to cardiomyocyte viability. With 3microM daunorubicin, the relative increase of AUC of cTnT and cTnI was 2.4- and 5.3-fold higher than the increase of LDH activity, respectively. In rabbits, the daunorubicin-induced cardiomyopathy was associated with progressive increase of both cTnT and cTnI. Although the correlation between cTnT and cTnI cumulative release (AUCs) was found (R=0.81; P<0.01) and both cardiac troponins corresponded well with the echocardiographically-assessed systolic dysfunction (R=0.83 and 0.81 for cTnT and cTnI, respectively; P<0.001), the first significant increase in cTnI levels was observed earlier (at a cumulative daunorubicin dose of 200mg/m(2)) than with cTnT (350mg/m(2)). In conclusion, our study has confirmed cTnT and cTnI as very sensitive and specific markers of anthracycline-induced cardiotoxicity. The troponins can become not only the bridge between the clinical and experimental studies of drug-induced cardiotoxicity but also the linkage between the preclinical experiments in vitro and in vivo.

Effects of Salviae Mitiorrhizae and Cortex Moutan extract on the rat heart after myocardial infarction: a proteomic study

In this study, we characterized the therapeutical effects of Salviae Mitiorrhizae (Danshen) and Cortex Moutan (Danpi) extract (SDD) on Sprague-Dawley rats subjected to coronary artery ligation, and applied proteomic approach to investigate its potential mechanism of action. The chemical composition of SDD was investigated by HPLC/MS(n) analysis. Measurement for serum levels of creatine kinase (CK), creatine kinase-MB (CK-MB), nitrite and histological study for infarct area of heart were performed. Moreover, protein abundance profiles of myocardium were compared by two-dimensional gel electrophoresis and altered proteins were identified by MALDI-TOF-MS. The results showed SDD significantly decreased CK, CK-MB concentration in serum and infarct area of heart, while increased the release of nitrite in rats with coronary occlusion. Increased concentration of ATP and total adenine nucleotide indicated the energy metabolism has been improved in ischemic heart induced by SDD. Proteomic data revealed that 23 proteins associated with energy metabolism, oxidative stress and cytoskeleton were modulated in SDD treated rats.

Myosin binding protein C is differentially phosphorylated upon myocardial stunning in canine and rat hearts — Evidence for novel phosphorylation sites

Myocardial stunning is the transient cardiac dysfunction that follows brief episodes of ischemia and reperfusion without associated myocardial necrosis. Currently, there is limited knowledge about its cellular and biochemical mechanisms. In order to better understand the underlying mechanisms of contractile dysfunction associated with the stunning, comprehensive proteomic studies using 2-D DIGE were performed using a regional stunning model in canine heart. Cardiac myosin binding protein C (cMyBP-C), a regulatory myofilament protein associated with the thick filament, and nebulette, a thin filament associated protein, were differentially expressed. Phosphoprotein specific staining indicated both protein changes were due to phosphorylation. Subsequent phosphorylation mapping of canine cMyBP-C using IMAC and MS/MS identified five phosphorylation sites, including three novel sites. In order to further evaluate this finding in a different model, cMyBP-C phosphorylation was examined in a rat model of global stunning. In the rat model, stunning was associated with increased phosphorylation of cMyBP-C at a critical calcium/calmodulin-dependent kinase II site, and the increased phosphorylation was largely inhibited when stunning was prevented by either ischemic preconditioning or reperfusion in the presence of low-calcium buffer. These data indicate cMyBP-C phosphorylation plays an important role in myocardial stunning.

Myocardial regulatory proteins and heart failure

Cardiac troponin T (cTnT) and cardiac troponin I (cTnI) are considered to be the most specific and sensitive biochemical markers of myocardial damage. Troponins have been studied in a wide range of clinical settings, including heart failure; however, there are few data on the role of regulatory proteins in the pathogenesis of heart failure, although a few interesting hypotheses have been proposed. A considerable body of evidence favours the view that alteration of the myocardial thin filament is the primary event leading to defective contractility of the failing myocardium, while the changes in Ca(2+) handling are a compensatory response. A better understanding of the role of regulatory proteins under different physiological and pathological conditions could lead to new therapeutic approaches in heart failure. Recently, calcium sensitisation has been proposed as a novel method by which cardiac performance may be enhanced via an increase in the affinity of troponin C for calcium but without affecting intracellular calcium concentration. To date, the only calcium sensitizer used in clinical practice is levosimendan.

Proteomic analysis of rat aorta during atherosclerosis induced by high cholesterol diet and injection of vitamin D3

1. Atherosclerosis (AS) in rats displays important clinical similarities to human AS. 2. After the experimental model of AS in rat was established and using a proteomic approach, we compared the protein profiling of aorta tissues from healthy and AS rats. 3. Using two-dimensional electrophoresis (2-DE), over 1878 protein species were separated; among them, 1239 protein spots were matched between different gels with average matching rate of approximately 66%. Gel analysis and protein characterization have identified 58 protein spots whose abundance is significantly altered in AS rats. 4. By using matrix-associated laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS) and NCBInr database, 46 proteins were successfully identified. Among them, 18 proteins were of increased abundance in diseased tissues including a group of oxidization-related enzymes such as peroxiredoxin2 and NADH dehydrogenase Fe-S protein 6, components of inflammatory pathways such as lamin A, while 28 proteins were of decreased abundance in the diseased state, including CaM-KII inhibitory protein, transferring, fructose-bisphosphate aldolase. 5. We believe that these results would give insights into the cellular and molecular mechanisms involved in AS development and might lead to the discovery of novel diagnostic markers and new therapeutic opportunities.

Troponin as a marker of myocardiac damage in drug-induced cardiotoxicity

Cardiac troponins T and I (cTnT and cTnI) are becoming the serum biomarkers of choice for monitoring potential drug-induced myocardial injury in both clinical and preclinical studies. The utility of cardiac troponins has been mainly demonstrated following the administration of antineoplastic drugs and beta-sympathomimetics, although the routine use of these markers in the monitoring in patients who received anthracyclines therapy is far from settled. Unlike the previous markers, which suffered from numerous shortages, the main advantages of cardiac troponins are their high specificity and sensitivity, wide diagnostic window and the possibility to use commercially available assays in clinical settings as well as in a broad range of laboratory animals. Nevertheless, in spite of vigorous research in this area, a number of questions are still unanswered and these are discussed in this review. The main problems seem to be the lack of standardisation of variety of troponin immunoassays, the assessment of suitable cutoff for drug-induced cardiotoxicity and determination of critical diagnostic window related to the optimal timing of sample collection, which may be drug-dependent.

Interaction proteomics

The term proteome is traditionally associated with the identification of a large number of proteins within complex mixtures originating from a given organelle, cell or even organism. Current proteome investigations are basically focused on two major areas, expression proteomics and functional proteomics. Both approaches rely on the fractionation of protein mixtures essentially by two-dimensional polyacrylamide gel electrophoresis (2D-gel) and the identification of individual protein bands by mass spectrometric techniques (2D-MS). Functional proteomics approaches are basically addressing two main targets, the elucidation of the biological function of unknown proteins and the definition of cellular mechanisms at the molecular level. In the cell many processes are governed not only by the relative abundance of proteins but also by rapid and transient regulation of activity, association and localization of proteins and protein complexes. The association of an unknown protein with partners belonging to a specific protein complex involved in a particular process would then be strongly suggestive of its biological function. The identification of interacting proteins in stable complexes in a cellular system is essentially achieved by affinity-based procedures. Different strategies relying on this simple concept have been developed and a brief overview of the main approaches presently used in functional proteomics studies is described.

Functional proteomics

BACKGROUND

With the increase in the number of genome sequencing projects, there is a concomitant exponential growth in the number of protein sequences whose function is still unknown. Functional proteomics constitutes an emerging research area in the proteomic field whose approaches are addressed towards two major targets: the elucidation of the biological function of unknown proteins and the definition of cellular mechanisms at the molecular level.

METHODS

The identification of interacting proteins in stable complexes in vivo is essentially achieved by affinity-based procedures. The basic idea is to express the protein of interest with a suitable tag to be used as a bait to fish its specific partners out from a cellular extract. Individual components within the multi-protein complex can then be identified by mass spectrometric methodologies.

RESULTS AND CONCLUSIONS

The association of an unknown protein with partners belonging to a specific protein complex involved in a particular mechanism is strongly suggestive of the biological function of the protein. Moreover, the identification of protein partners interacting with a given protein will lead to the description of cellular mechanisms at the molecular level. The next goal will be to generate animal models bearing a tagged form of the bait protein.

Comparative analysis of the proteome of left ventricular heart of arteriosclerosis in rat

Despite the worldwide occurrence of coronary atherosclerotic heart disease (CAHD), the pathogenic mechanisms underlying this disease remain largely unknown. In this study, the experimental model of atherosclerosis in rat (CAHD rat) was established by the injection of vitamin D3 associated with high fat diet for 6 weeks. By using the proteomic approach, we comparatively analyzed the proteome of the control and CAHD rat left ventricular myocardial tissues. We reproducibly separated over 2500 polypeptides by using two-dimensional electrophoresis (2-DE) at pH range of 3-11. Among these proteins, 26 proteins with large amount were identified using micro high performance liquid chromatography mass spectrometer/mass spectrometer (micro-HPLC-MS/MS). Using PDQUEST software to process the 2-DE gel images, 38 protein spots that significantly altered in CAHD were detected. Of these, 12 proteins were identified with high confidence by using 2-DE and matrix-associated laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS). The identification of protein alterations specify to CAHD would clarify the pathogenetic mechanisms involved in the disease and might be of prognostic and therapeutic benefit.

Proteomics

Proteomics is the measurement of one or more protein populations or proteomes, preferably in a quantitative manner. A protein population may be the set of proteins found in an organism, in a tissue or biofluid, in a cell, or in a subcellular compartment. A population also may be the set of proteins with a common characteristic, for example, those that interact with each other in molecular complexes, those involved in the same process such as signal transduction or cell cycle control, or those that share a common posttranslational modification such as phosphorylation or glycosylation. Proteomics experiments that involve mass spectrometry are divided into five categories: (1) protein identification, (2) protein quantitation or differential analysis, (3) protein-protein interactions, (4) post-translational modifications, and (5) structural proteomics. Each of these proteomics categories is reviewed. Examples are given for quantitative experiments involving two-dimensional gel electrophoresis, and for gel-free analysis using isotope-coded affinity tags. The impact of proteomics on biological research and on drug development is discussed. Challenges for further development in proteomics are presented, including sample preparation, sensitivity, dynamic range, and automation.

Cardiac mitochondrial damage and biogenesis in a chronic model of type 1 diabetes

Diabetic cardiomyopathy is a common complication leading to heightened risk of heart failure and death. In the present report, we performed proteomic analysis on total cardiac proteins from the OVE26 mouse model of type 1 diabetes to identify protein changes that may contribute to diabetic cardiomyopathy. This analysis revealed that a surprising high proportion (12 of 20) of the altered proteins that could be identified by mass spectrometry were of mitochondrial origin. All but one of these proteins were upregulated by diabetes. Quantitative RT-PCR, performed for two of these proteins, indicated that part of the upregulation was attributed to increased messenger RNA levels. Morphological study of diabetic hearts showed significantly increased mitochondrial area and number as well as focal regions with severe damage to mitochondria. Diabetic mitochondria also showed reduced respiratory control ratio (9.63 +/- 0.20 vs. 6.13 +/- 0.41, P < 0.0001), apparently due to reduced state 3 rate, and diminished GSH level (5.5 +/- 0.9 vs. 8.2 +/- 2.5 micromol/mg protein, P < 0.05), indicating impaired mitochondrial function and increased oxidative stress. Further examination revealed increased mitochondrial DNA (1.03 +/- 0.18 vs. 0.69 +/- 0.13 relative copy number, P < 0.001) and a tendency to higher protein yield in OVE26 cardiac mitochondria, as well as increased mRNA level for mitochondrial transcription factor A and two mitochondrial encoded proteins. Taken together, these results show that mitochondria are a primary target in the diabetic heart, probably due to oxidative stress, and that this damage coincides with and may stimulate mitochondrial biogenesis.

High throughput approaches in neuroscience

Traditional approaches to understanding biological problems are now being advanced with the use of high throughput technologies, which analyse multiple samples simultaneously, or thousands of analytes in a single sample. The application of these technologies in neurochemistry and neuroscience is beginning to be explored and is assisting in the development of new models of drug action, neuroanatomical investigations, and in identifying molecular pathways involved in neurological and psychiatric disease. Tools such as microarray-based gene expression profiling and 2D and multidimensional proteomic methods are uncovering functional components to a wide variety of neuroscience paradigms and the application of these technologies is set to become standard in analysis.

Functional genomics and proteomics: application in neurosciences

The sequencing of the complete genome for many organisms, including man, has opened the door to the systematic understanding of how complex structures such as the brain integrate and function, not only in health but also in disease. This blueprint, however, means that the piecemeal analysis regimes of the past are being rapidly superseded by new methods that analyse not just tens of genes or proteins at any one time, but thousands, if not the entire repertoire of a cell population or tissue under investigation. Using the most appropriate method of analysis to maximise the available data therefore becomes vital if a complete picture is to be obtained of how a system or individual cell is affected by a treatment or disease. This review examines what methods are currently available for the large scale analysis of gene and protein expression, and what are their limitations.

Proteomics in pancreatic disease

Proteomics represents a novel methodological approach to investigate the expression of all proteins by a cell or organism in its entireness, similar to global strategies for DNA (genomics) and RNA (transcriptomics). This review focuses on the history of protein analysis, which made up the golden age of pancreatic physiology, the current methodology for proteomics (2D gel electrophoresis, mass spectrometry) and the few published experiences with proteomics in the field of pancreatology until now. Finally, potential applications of proteomics for the pancreas, in concert with other techniques, are cited.

Analysis of expression and posttranslational modification of proteins during hypoxia

The cellular responses to hypoxia are complex and characterized by alterations in the expression of a number of genes, including stress-related genes and corresponding proteins that are necessary to maintain homeostasis. The purpose of this article is to review previous and recent studies that have examined the changes in the expression and posttranslational modification of proteins in response to chronic sustained and intermittent forms of hypoxia. A large number of studies focused on the analysis of either the single protein or a subset of related proteins using one-dimensional gel electrophoresis to separate a complex set of proteins from solubilized tissues or cell extracts, followed by immunostaining of proteins using antibodies that are specific to either native or posttranslationally modified forms. On the other hand, only a limited number of studies have examined the global perturbations on protein expression by hypoxia using proteomics approach involving two-dimensional electrophoresis coupled with mass spectrometry. Results derived from specific protein analysis of a variety of tissues and cells showed that hypoxia, depending on the duration and severity of the stimulus, affects the level and the state of posttranslational modification of a subset of proteins that are associated with energy metabolism, stress response, cell injury, development, and apoptosis. Some of these earlier findings are further corroborated by recent studies that utilize a global proteomics approach, and, more importantly, results from these proteomics investigations on the effects of hypoxia provide new protein targets for further functional analysis. The anticipated new information stems from the analysis of expression, and posttranslational modification of these novel protein targets, along with gene expression profiles, offers exciting new opportunities to further define the mechanisms of cellular responses to hypoxia and to control more effectively the clinical consequences of prolonged or periodic lack of oxygen.

Identification of Novel Signaling Complexes by Functional Proteomics

The rapid development of proteomic technologies, combined with the completion of the Human Genome Map, has enabled the compiling of an unprecedented inventory of cellular proteins. Functional proteomics is an emerging field that aims to utilize the enormous amount of information provided by these proteomic technologies to understand the functions of cellular proteins. The utility of functional proteomics has been recently exploited to elucidate cellular mechanisms in numerous fields, of particular salience in the area of signal transduction. This review presents a functional proteomic approach for the study of cardiac cell signaling. It illustrates the strategies by which the subproteome of a targeted signaling system is characterized in an unbiased fashion, the manner in which the biochemical functions of this subproteome are assessed using established molecular and protein chemistry methods, and the challenges associated with these studies.

Proteomics in biomarker discovery and drug development

Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time can be considered in an integrated way. Proteomic technology has been extensively used to tackle a wide variety of medical subjects including biomarker discovery and drug development. By complement with other new technique advances in genomics and bioinformatics, proteomics has a great potential to make considerable contribution to biomarker identification and to revolutionize drug development process. This article provides a brief overview of the proteomic technologies and their application in biomarker discovery and drug development.

[Proteomics and cardiovascular disease]

The description of the human genome has opened new venues for the study and understanding of pathophysiological phenomena. In the 20th century, individual cell components were studied. The 21st century began with a global analysis of cell components. Thanks to the development of new technologies such as DNA chips, or two-dimensional electrophoresis, we can now study the expression of thousands of genes, or the proteins they encode, in a few hours. Genomics has opened the way for proteomics. Improved knowledge of genes does not provide information about cell functions, because any cell expresses all genes simultaneously. Instead, there is selective gene expression depending on the cell type and the stimuli to which it is exposed. The result of this is the proteome, an ensemble of proteins that are responsible for cell functions at any given moment, which are the object of the study of proteomics. The description of the proteome of cardiac cells has begun and some new proteins have been found to be dysregulated in different cardiomyopathies. These proteins are involved either in energy production or in the stress response, or belong to the cell proteasome or cytoskeleton. They may be potential risk markers or new therapeutic targets in the future. In this sense, chemogenomics is a new methodology for the development of new drugs using genomic and proteomic data.

Functional proteomics to study protection of the ischaemic myocardium

Mechanisms to reduce the deleterious effects of myocardial ischaemia are of particular clinical importance and have been the focus of intense research for a number of years. Among novel approaches to studying the ischaemic heart, proteomics, or the analysis of all cellular proteins, presents as a powerful method to deconstruct the mechanisms of disease and protection. Specifically, the field of functional proteomics is an emerging application of proteomics that melds aspects of classical proteomics, biochemistry, molecular biology and physiology into an approach that facilitates an understanding of how proteins and protein interactions engender phenotype. This review highlights different types of proteomic applications and provides a prospectus for functional proteomics as a robust vehicle driving drug discovery and design.

Protein kinase C epsilon signaling complexes include metabolism- and transcription/translation-related proteins: complimentary separation techniques with LC/MS/MS

The serine/threonine kinase protein kinase C epsilon (PKC epsilon) has been shown to be a critical component in the heart's resistance to cell death following ischemic insult. Recent studies have indicated that PKC epsilon forms multi-protein signaling complexes to accomplish signal transduction in cardiac protection. Using two-dimensional electrophoresis (2DE), combined with matrix-assisted laser desorption ionization mass spectrometry (MS), the initial analysis of these complexes identified signaling molecules, structural proteins, and stress-activated proteins. The initial analysis, although fruitful, was limited by the number of proteins revealed on the 2D gels. It was also apparent that many known cardiac protective functions of PKC epsilon could not be fully accounted for by the proteins identified in the initial analysis. Here we reported the identification of an additional 57 proteins in PKC epsilon complexes using complimentary separation techniques, combined with high sensitivity MS. These techniques include 2DE or large format 1D SDS-PAGE followed by LC/MS/MS and solution trypsin digestion followed by LC/MS/MS, all of which yielded novel data regarding PKC epsilon protein complexes. Nanoscale LC/MS/MS for the analysis of gel-isolated proteins was performed with sub-femtomole sensitivity. In contrast to 2DE analyses, the identification of proteins from 1D gels was independent of their visualization via staining and allowed for the identification of proteins with high isoelectric points. We found that PKC epsilon complexes contain numerous structural and signaling molecules that had escaped detection by our previous analyses. Most importantly, we identified two new groups of proteins that were previously unrecognized as components of the PKC epsilon complex: metabolism-related proteins and transcription/translation-related proteins.

Separation and identification of human heart proteins

Heart failure is not a uniform disease entity, but a syndrome with various causes, including hypertension, ischemia and congenital heart disease, cardiomyopathy, myocarditis and intoxication. During the recent years a number of molecular and cellular alterations have been identified in the diseased heart, but a direct causative link between these changes and functional impairment, medical responsiveness, progression of the disease and the patients' outcome remains to be established. After an accumulation of large amounts of DNA sequence data in genomic projects, scientists have now turned their attention to the central executors of all programs of life, the proteins. In complementation of the genomic initiatives, proteomics based approaches have lined up not only for large-scale identification of proteins and their post-translational modifications, but also to study the function of protein complexes, protein-protein interactions and regulatory and signalling cascades in the cellular network. In concert with genomic data functional proteomics will hold the key for a better understanding and therapeutical management of cardiovascular diseases in the future.

Molecular biologist's guide to proteomics

The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems.

The role of troponin abnormalities as a cause for stunned myocardium

Myocardial stunning is a form of ischemic injury, which occurs with transient ischemia followed by re-establishment of flow, and which results in reversible cardiac dysfunction. There is evidence that the molecular defect in stunning is at the level of the contractile apparatus. Selective proteolysis of the myofilament protein, troponin I, appears to underlie the phenotype of stunning in some models, but other myofilament protein modifications may also have a role.

Cardiovascular proteomics: evolution and potential

The development of proteomics is a timely one for cardiovascular research. Analyses at the organ, subcellular, and molecular levels have revealed dynamic, complex, and subtle intracellular processes associated with heart and vascular disease. The power and flexibility of proteomic analyses, which facilitate protein separation, identification, and characterization, should hasten our understanding of these processes at the protein level. Properly applied, proteomics provides researchers with cellular protein "inventories" at specific moments in time, making it ideal for documenting protein modification due to a particular disease, condition, or treatment. This is accomplished through the establishment of species- and tissue-specific protein databases, providing a foundation for subsequent proteomic studies. Evolution of proteomic techniques has permitted more thorough investigation into molecular mechanisms underlying cardiovascular disease, facilitating identification not only of modified proteins but also of the nature of their modification. Continued development should lead to functional proteomic studies, in which identification of protein modification, in conjunction with functional data from established biochemical and physiological methods, has the ability to further our understanding of the interplay between proteome change and cardiovascular disease.

Use of functional proteomics to investigate PKC epsilon-mediated cardioprotection: the signaling module hypothesis

The characterization of biological processes on the basis of alterations in the cellular proteins, or "proteomic" analysis, is a powerful approach that may be adopted to decipher the signaling mechanisms that underlie various pathophysiological conditions, such as ischemic heart disease. This review represents a prospectus for the implementation of proteomic analyses to delineate the myocardial intracellular signaling events that evoke cardioprotection against ischemic injury. In concert with this, the manifestation of a protective phenotype has recently been shown to involve dynamic modulation of protein kinase C-epsilon (PKC epsilon) signaling complexes (Ping P, Zhang J, Pierce WM Jr, and Bolli R. Circ Res 88: 59--62, 2001). Accordingly, "the signaling module hypothesis" is formulated as a plausible mechanism by which multipurpose stress-activated proteins and signaling kinases may function collectively to facilitate the genesis of cardioprotection.

DNA technology, the clinical laboratory, and the future

OBJECTIVE

To review the advances in clinically useful molecular biological techniques and their applications in clinical practice as presented at the Ninth Annual William Beaumont Hospital DNA Symposium.

DATA SOURCES

The 10 manuscripts submitted were reviewed and their major findings were compared with literature on the same topic.

STUDY SELECTION

One manuscript reviewed the development of pharmacogenetics, 3 described analytic approaches to detect aneuploidy or cancer, 1 described transcription factor E2F-1 increase during apoptosis, 2 reported on genetic and pharmacologic factors that influence platelet aggregation, 2 described molecular methods for detecting long QT syndrome or mycobacteria, and 1 reported a modification in collection of buccal DNA.

DATA SYNTHESIS

Genomic and proteomic approaches to develop clinically useful assays have been successful. Aneuploidy can be easily detected by comparative genomic hybridization, which does not require cell culture like cytogenetics. Mutations have been characterized for a variety of hereditary cancer syndromes, 2 inherited long QT syndromes, and thromboembolism. PlA1 and PlA2 polymorphisms in platelets are associated with a difference in aggregation inhibition by estrogen, another example of genotypic pharmacogenetics. Protein expression differences may define colorectal cancer stage and explain apoptotic signal transduction. Mycobacterial detection by nucleic acid amplification and simplified buccal DNA collection demonstrate cost-effective strategies.

CONCLUSION

The working draft of the Human Genome Project is completed and the number of clinically useful molecular pathologic techniques and assays will expand as additional disease-associated mutations are defined. Expanded use of database software for genomic and proteomic screening should increase the efficiency of clinical useful assay development.

Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics

Novel and powerful technologies such as DNA microarrays and proteomics have made possible the analysis of the expression levels of multiple genes simultaneously both in health and disease. In combination, these technologies promise to revolutionize biology, in particular in the area of molecular medicine as they are expected to reveal gene regulation events involved in disease progression as well as to pinpoint potential targets for drug discovery and diagnostics. Here, we review the current status of these technologies and highlight some studies in which they have been applied in concert to the analysis of biopsy specimens.

Proteomics: applications in basic and applied biology

The rapid evolution of proteomics has continued during the past year, with a series of innovations in the core technologies of two-dimensional electrophoresis and mass spectrometry, and a diversity of productive research programmes. Well-annotated proteomics databases are now emerging in a number of fields to provide a platform for systematic research, with particularly promising progress in clinical applications such as cardiology and oncology. Large-scale quantitative research, comparable in power and sensitivity to that achieved for gene expression, is thus becoming a reality at the protein level.