Proteomics and metabolomics in biomarker discovery for cardiovascular diseases: progress and potential

N, Adigal S, Lukose J, Kartha VB, Chidangil S. Cardiovascular biomarkers in body fluids: progress and prospects in optical sensors

Cardiovascular diseases (CVD) are the major causative factors for high mortality and morbidity in developing and developed nations. The biomarker detection plays a crucial role in the early diagnosis of several non-infectious and life-threatening diseases like CVD and many cancers, which in turn will help in more successful therapy, reducing the mortality rate. Biomarkers have diagnostic, prognostic and therapeutic significances. The search for novel biomarkers using proteomics, bio-sensing, micro-fluidics, and spectroscopic techniques with good sensitivity and specificity for CVD is progressing rapidly at present, in addition to the use of gold standard biomarkers like troponin. This review is dealing with the current progress and prospects in biomarker research for the diagnosis of cardiovascular diseases.

Expert opinion.

Fast diagnosis of cardiovascular diseases (CVDs) can help to provide rapid medical intervention, which can affect the patient’s short and long-term health. Identification and detection of proper biomarkers for early diagnosis are crucial for successful therapy and prognosis of CVDs. The present review discusses the analysis of clinical samples such as whole blood, blood serum, and other body fluids using techniques like high-performance liquid chromatography-LASER/LED-induced fluorescence, Raman spectroscopy, mainly, optical methods, combined with nanotechnology and micro-fluidic technologies, to probe patterns of multiple markers (marker signatures) as compared to conventional techniques.

Proteomics of restenosis model in LDLR-deficient hamsters coupled with the proliferative rat vascular smooth muscle cells reveals a new mechanism of vascular remodeling diseases

A major pathological mechanism involved in vascular remodeling diseases is the proliferation and migration of vascular smooth muscle cells. The lipid distribution of golden hamsters is similar to that of humans, which makes them an excellent study model for studying the pathogenesis and molecular characteristics of vascular remodeling diseases. We performed proteomic analysis on Sprague Dawley rat VSMCs (rVSMCs) and restenosis hamsters with low-density lipoprotein receptor (LDLR) deficiency as part of this study. We have also performed the enrichment analysis of differentially modified proteins in regards to Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein domain. 1070 differentially abundant proteins were assessed in rVSMCs before and after platelet-derived growth factor-BB (PDGF-BB) stimulation. Specifically, 1246 proteins displayed significant differences in the restenosis model in LDLR-deficient hamsters. An analysis of crosstalk between LDLR^+/- hamsters artery restenosis and proliferating rVSMCs revealed 130 differentially expressed proteins, including 67 up-regulated proteins and 63 downregulated proteins. Enrichment analysis with KEGG showed differential proteins to be mainly concentrated in metabolic pathways. There are numerous differentially abundant proteins but particularly two proteins (phosphofructokinase 1 of liver type and lactate dehydrogenase A) were found to be up-regulated by PDGF-BB stimulation of rVSMCs and in a restenosis model of hamsters with LDLR^+/- expression. SIGNIFICANCE: Based on bioinformatics, we have found glycolysis pathway plays an important role in both the LDLR^+/- hamsters restenosis model and the proliferation of rVSMCs. Some key glycolysis enzymes may likely be developed either as new biomarkers or drug targets for vascular remodeling diseases.

Clinical Phenotypes of Cardiovascular and Heart Failure Diseases Can Be Reversed? The Holistic Principle of Systems Biology in Multifaceted Heart Diseases

Recent advances in cardiology and biological sciences have improved quality of life in patients with complex cardiovascular diseases (CVDs) or heart failure (HF). Regardless of medical progress, complex cardiac diseases continue to have a prolonged clinical course with high morbidity and mortality. Interventional coronary techniques together with drug therapy improve quality and future prospects of life, but do not reverse the course of the atherosclerotic process that remains relentlessly progressive. The probability of CVDs and HF phenotypes to reverse can be supported by the advances made on the medical holistic principle of systems biology (SB) and on artificial intelligence (AI). Studies on clinical phenotypes reversal should be based on the research performed in large populations of patients following gathering and analyzing large amounts of relative data that embrace the concept of complexity. To decipher the complexity conundrum, a multiomics approach is needed with network analysis of the biological data. Only by understanding the complexity of chronic heart diseases and explaining the interrelationship between different interconnected biological networks can the probability for clinical phenotypes reversal be increased.

Association of Serum β-Hydroxybutyrate and Coronary Artery Disease in an Urban Chinese Population

Ketone bodies, including β-hydroxybutyrate (BHB), acetoacetate (AA), and acetone, can substitute and alternate with glucose under conditions of fuel/food deficiency. Ketone-body metabolism is increased in a myriad of tissue-metabolism disorders. Perturbations in metabolism are major contributors to coronary artery disease (CAD). We investigated the association of BHB with CAD. A total of 2,970 people of Chinese Han ethnicity were enrolled. The Gensini score was calculated for all patients who had positive findings. The serum level of BHB and other laboratory parameters were measured. The association of serum levels of metabolites with traditionally risk factors and CAD severity was analyzed. The BHB was found to be associated with some traditional risk factors of CAD and CAD severity, as determined by the Gensini score or the number of diseased regions. Moreover, BHB was associated with the T3/T1 tertiles of the Gensini score after the adjustment for traditional risk factors by multivariable logistic regression analysis. The association of BHB with CAD severity was more obvious in women. Taken together, these data suggest that the circulating BHB level is independently associated with CAD severity, and that this association is more pronounced in women.

Cardiac function dependence on carbon monoxide

Nitric oxide, studied to evaluate its role in cardiovascular physiology, has cardioprotective and therapeutic effects in cellular signaling, mitochondrial function, and in regulating inflammatory processes. Heme oxygenase (major role in catabolism of heme into biliverdin, carbon monoxide (CO), and iron) has similar effects as well. CO has been suggested as the molecule that is responsible for many of the above mentioned cytoprotective and therapeutic pathways as CO is a signaling molecule in the control of physiological functions. This is counterintuitive as toxic effects are related to its binding to hemoglobin. However, CO is normally produced in the body. Experimental evidence indicates that this toxic gas, CO, exerts cytoprotective properties related to cellular stress including the heart and is being assessed for its cytoprotective and cytotherapeutic properties. While survival of adult cardiomyocytes depends on oxidative phosphorylation (survival and resulting cardiac function is impaired by mitochondrial damage), mitochondrial biogenesis is modified by the heme oxygenase-1/CO system and can result in promotion of mitochondrial biogenesis by associating mitochondrial redox status to the redox-active transcription factors. It has been suggested that the heme oxygenase-1/CO system is important in differentiation of embryonic stem cells and maturation of cardiomyocytes which is thought to mitigate progression of degenerative cardiovascular diseases. Effects on other cardiac cells are being studied. Acute exposure to air pollution (and, therefore, CO) is associated with cardiovascular mortality, myocardial infarction, and heart failure, but changes in the endogenous heme oxygenase-1 system (and, thereby, CO) positively affect cardiovascular health. We will review the effect of CO on heart health and function in this article.

Complement C5 Protein as a Marker of Subclinical Atherosclerosis

BACKGROUND

The mechanisms underlying early atherosclerotic plaque formation are not completely understood. Moreover, plasma biomarkers of subclinical atherosclerosis are lacking.

OBJECTIVES

The purpose of this study was to analyze the temporal and topologically resolved protein changes taking place in human aortas with early atherosclerosis to find new potential diagnostic and/or therapeutic targets.

METHODS

The protein composition of healthy aortas (media layer) or with early atheroma (fatty streak and fibrolipidic, media and intima layers) was analyzed by deep quantitative multiplexed proteomics. Further analysis was performed by Western blot, immunohistochemistry, real-time polymerase chain reaction, and enzyme-linked immunosorbent assay. Plasma levels of complement C5 were analyzed in relation to the presence of generalized (>2 plaques) or incipient (0 to 2 plaques) subclinical atherosclerosis in 2 independent clinical cohorts (PESA [Progression of Early Subclinical Atherosclerosis] [n = 360] and NEFRONA [National Observatory of Atherosclerosis in Nephrology] [n = 394]).

RESULTS

Proteins involved in lipid transport, complement system, immunoglobulin superfamily, and hemostasis are increased in early plaques. Components from the complement activation pathway were predominantly increased in the intima of fibrolipidic plaques. Among them, increased C5 protein levels were further confirmed by Western blot, enzyme-linked immunosorbent assay and immunohistochemistry, and associated with in situ complement activation. Plasma C5 was significantly increased in individuals with generalized subclinical atherosclerosis in both PESA and NEFRONA cohorts, independently of risk factors. Moreover, in the PESA study, C5 plasma levels positively correlated with global plaque volume and coronary calcification.

CONCLUSIONS

Activation of the complement system is a major alteration in early atherosclerotic plaques and is reflected by increased C5 plasma levels, which have promising value as a novel circulating biomarker of subclinical atherosclerosis.

UHPLC-QTOFMS-based metabolomic analysis of serum and urine in rats treated with musalais containing varying ethyl carbamate content

The aim of this work is to investigate the effect of the ethyl carbamate (EC) content in musalais on the metabolism of rats. Electron beam irradiation was performed to decrease the content of EC in musalais, and Sprague Dawley rats were subjected to intragastric administration of musalais with varying EC content (high, medium, and low groups). Control rats were fed normally without any treatment. Serum and urine samples were analyzed using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry. Principal component analysis and orthogonal projections to latent structures discriminant analysis (OPLS-DA) were performed to detect changes in the metabolite profile in the serum and urine in order to identify the differential metabolites and metabolic pathways. The results demonstrated clear differences in the serum and urine metabolic patterns between control and treatment groups. Ions in treatment groups with variable importance in the projection of >1 (selected from the OPLS-DA loading plots) and Ps < 0.05 (Student t test) compared to control group were identified as candidate metabolites. Analysis of the metabolic pathways relevant to the identified differential metabolites revealed that high EC content in musalais (10 mg/kg) mainly affected rats through valine, leucine, and isoleucine biosynthesis and nicotinate and nicotinamide metabolism, which were associated with energy metabolism. In addition, this work suggests that EC can induce oxidative stress via inhibition of glycine content.

Metabolic profiling and novel plasma biomarkers for predicting survival in epithelial ovarian cancer

Epithelial ovarian cancer (EOC) is one of the most lethal gynecological malignancies around the world, and patients with ovarian cancer always have an extremely poor chance of survival. Therefore, it is meaningful to develop a highly efficient model that can predict the overall survival for EOC. In order to investigate whether metabolites could be used to predict the survival of EOC, we performed a metabolic analysis of 98 plasma samples with follow-up information, based on the ultra-performance liquid chromatography mass spectrometry (UPLC/MS) systems in both positive (ESI+) and negative (ESI-) modes. Four metabolites: Kynurenine, Acetylcarnitine, PC (42:11), and LPE(22:0/0:0) were selected as potential predictive biomarkers. The AUC value of metabolite-based risk score, together with pathological stages in predicting three-year survival rate was 0.80. The discrimination performance of these four biomarkers between short-term mortality and long-term survival was excellent, with an AUC value of 0.82. In conclusion, our plasma metabolomics study presented the dysregulated metabolism related to the survival of EOC, and plasma metabolites could be utilized to predict the overall survival and discriminate the short-term mortality and long-term survival for EOC patients. These results could provide supplementary information for further study about EOC survival mechanism and guiding the appropriate clinical treatment.

Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart

Despite advances in myocardial reperfusion therapies, acute myocardial ischaemia/reperfusion injury and consequent ischaemic heart failure represent the number one cause of morbidity and mortality in industrialized societies. Although different therapeutic interventions have been shown beneficial in preclinical settings, an effective cardioprotective or regenerative therapy has yet to be successfully introduced in the clinical arena. Given the complex pathophysiology of the ischaemic heart, large scale, unbiased, global approaches capable of identifying multiple branches of the signalling networks activated in the ischaemic/reperfused heart might be more successful in the search for novel diagnostic or therapeutic targets. High-throughput techniques allow high-resolution, genome-wide investigation of genetic variants, epigenetic modifications, and associated gene expression profiles. Platforms such as proteomics and metabolomics (not described here in detail) also offer simultaneous readouts of hundreds of proteins and metabolites. Isolated omics analyses usually provide Big Data requiring large data storage, advanced computational resources and complex bioinformatics tools. The possibility of integrating different omics approaches gives new hope to better understand the molecular circuitry activated by myocardial ischaemia, putting it in the context of the human ‘diseasome’. Since modifications of cardiac gene expression have been consistently linked to pathophysiology of the ischaemic heart, the integration of epigenomic and transcriptomic data seems a promising approach to identify crucial disease networks. Thus, the scope of this Position Paper will be to highlight potentials and limitations of these approaches, and to provide recommendations to optimize the search for novel diagnostic or therapeutic targets for acute ischaemia/reperfusion injury and ischaemic heart failure in the post-genomic era.

Sandwich NP-based biobarcode assay for quantification C-reactive protein in plasma samples

A NP-based biobarcode for C-reactive protein (CRP) quantification in plasma samples is reported for the first time. The assay uses capture antibody functionalized magnetic beads (pAbCRP2-MP), multifunctional oligonucleotide encoded probes modified with a detection antibody (pAbCRP1-ePSP), and a fluorescent DNA microarray. Thus, magnetic beads are added to the sample to form immunocomplexes that will be isolated, to then add the codified particles to form a sandwich complex with both particles and the target protein, subsequently the complexes are treated to release the oligonucleotide codes, which are finally hybridized in a fluorescent DNA microarray. The assay has been implemented to the analysis of plasma samples being able to quantify this biomarker within 900 ng mL^-1 to 12500 ng mL^-1 with an excellent accuracy (mean of recovery of 99.5 ± 4.2%, N = 3). The CRP biobarcode has been used on a small pilot clinical study in which plasma samples from patients suffering different pathologies, most of them related to cardiovascular diseases (CVDs). The samples have been analyzed and the results compared to a reference method demonstrating that the assay can be useful for monitoring this biomarker on patients being suspicious to be under risk of suffering CVDs or other diseases involving inflammatory processes.