The application of proteomics technology to thrombosis research: the identification of potential therapeutic targets in cardiovascular disease

Identifying novel biomarkers using proteomics to predict cancer-associated thrombosis

Comprehensive protein analyses of plasma are made possible by high-throughput proteomic screens, which may help find new therapeutic targets and diagnostic biomarkers. Patients with cancer are frequently affected by venous thromboembolism (VTE). The limited predictive accuracy of current VTE risk assessment tools highlights the need for new, more targeted biomarkers. Although coagulation biomarkers for the diagnosis, prognosis, and treatment of VTE have been investigated, none of them have the necessary clinical validation or diagnostic accuracy. Proteomics holds the potential to uncover new biomarkers and thrombotic pathways that impact the risk of thrombosis. This review explores the fundamental methods used in proteomics and focuses on particular biomarkers found in VTE and cancer-associated thrombosis.

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.

Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism

Background

It is well known that fibrin network binds a large variety of proteins, including inhibitors and activators of fibrinolysis, which may affect clot properties, such as stability and susceptibility to fibrinolysis. Specific plasma clot composition differs between individuals and may change in disease states. However, the plasma clot proteome has not yet been in-depth analyzed, mainly due to technical difficulty related to the presence of a highly abundant protein—fibrinogen and fibrin that forms a plasma clot.

Methods

The aim of our study was to optimize quantitative proteomic analysis of fibrin clots prepared ex vivo from citrated plasma of the peripheral blood drawn from patients with prior venous thromboembolism (VTE). We used a multiple enzyme digestion filter aided sample preparation, a multienzyme digestion (MED) FASP method combined with LC–MS/MS analysis performed on a Proxeon Easy-nLC System coupled to the Q Exactive HF mass spectrometer. We also evaluated the impact of peptide fractionation with pipet-tip strong anion exchange (SAX) method on the obtained results.

Results

Our proteomic approach revealed 476 proteins repeatedly identified in the plasma fibrin clots from patients with VTE including extracellular vesicle-derived proteins, lipoproteins, fibrinolysis inhibitors, and proteins involved in immune responses. The MED FASP method using three different enzymes: LysC, trypsin and chymotrypsin increased the number of identified peptides and proteins and their sequence coverage as compared to a single step digestion. Peptide fractionation with a pipet-tip strong anion exchange (SAX) protocol increased the depth of proteomic analyses, but also extended the time needed for sample analysis with LC–MS/MS.

Conclusions

The MED FASP method combined with a label-free quantification is an excellent proteomic approach for the analysis of fibrin clots prepared ex vivo from citrated plasma of patients with prior VTE.

Electronic supplementary material

The online version of this article (10.1186/s12014-017-9173-x) contains supplementary material, which is available to authorized users.

Shotgun analysis of plasma fibrin clot-bound proteins in patients with acute myocardial infarction

INTRODUCTION

The presence and amount of the proteins within a plasma clot may influence clot properties, like susceptibility to fibrinolysis, however, the clot proteome has not yet been extensively described. The aim of the study was to investigate the protein composition of clots of four patients with acute myocardial infarction (AMI) in two time points: in the acute ischemic phase and two months later during the standard therapy.

MATERIALS AND METHODS

Shotgun proteomic method (2DLC-MS/MS) was used to investigate time-dependent protein composition changes of clots prepared ex vivo from citrated plasma of the peripheral blood of patients with AMI.

RESULTS

Proteomic analysis revealed a total number of 62 proteins identified in all 8 samples grouping into several distinct functional clusters (e.g. cholesterol transporter activity, immunoglobulin binding and peptidase regulatory activity). The protein signatures of clots differed significantly depending on time after ACS, showing 30% greater variability in protein composition of the clots prepared in the plasma two months after the onset of AMI. Several proteins potentially involved in clot formation and resolution showed an interesting pattern of changes over time.

CONCLUSION

We provided the first qualitative analysis of proteomes of fibrin clots generated ex vivo in plasma taken from patients with AMI showing differences between clots generated in the acute ischemic phase and those prepared two months later. It might be hypothesized that differences involving proteins of potential influence on within-clot fibrinolysis and clot stability may partially explain time-dependent changes in the clots structure and firmness in patients with AMI.

Body fluid biomarkers in multiple sclerosis: how far we have come and how they could affect the clinic now and in the future

Multiple sclerosis (MS) is an autoimmune inflammatory disease of the central nervous system, which affects over 2.5 million people worldwide. Although MS has been extensively studied, many challenges still remain in regards to treatment, diagnosis and prognosis. Typically, prognosis and individual responses to treatment are evaluated by clinical tests such as the expanded disability status scale, MRI and presence of oligoclonal bands in the cerebrospinal fluid. However, none of these measures correlates strongly with treatment efficacy or disease progression across heterogeneous patient populations and subtypes of MS. Numerous studies over the past decades have attempted to identify sensitive and specific biomarkers for diagnosis, prognosis and treatment efficacy of MS. The objective of this article is to review and discuss the current literature on body fluid biomarkers in MS, including research on potential biomarker candidates in the areas of miRNA, mRNA, lipids and proteins.

Proteomic analysis of venous thromboembolism: an update

Venous thromboembolism is a complex, multifactorial disorder, the pathogenesis of which typically involves a variety of inherited or acquired factors. The multifactorial etiology of this disease and the partial correlation between genotype and prothrombotic phenotype limit greatly the value of genetic analysis in assessing thrombotic risk. The integration of several new 'omics' techniques enables a multifaceted and holistic approach to the study of venous thrombotic processes and pave the way to the search and identification of novel blood biomarkers and/or effectors of thrombus formation that can also be the possible future target of new anticoagulant and thrombolytic therapies for more personalized medicine. This review provides a comprehensive overview of the latest candidate proteomic biomarkers of venous thrombosis and of the proteomics studies relevant to its pathophysiology, some of which seem to confirm the existence of a common physiopathological basis for venous thromboembolism and atherothrombosis.

An update on markers of carotid atherosclerosis in patients with Type 2 diabetes

Carotid atherosclerosis constitutes an important cause of ischemic brain attack and stroke, accounting for up to 40% of cases of ischemic cerebrovascular disease. Type 2 diabetes mellitus is an independent risk factor for stroke and its recurrence. Thus, identifying diabetic patients who are at high risk of developing stroke is of great clinical importance. Noninvasive measurements of surrogate markers of atherosclerosis, such as novel serum biomarkers, can be helpful in detecting subclinical carotid disease, especially among individuals at the highest cardio-/cerebro-vascular risk. Previous studies have proposed an expanding body of serum biomarkers, such as C-reactive protein, fibrinogen, adipokines, cytokines and growth factors, as novel indicators of carotid atherosclerosis development that predict carotid-related clinical outcomes. Furthermore, those biomarkers are expected to assess the efficacy of both pharmaceutical and interventional strategies. Accordingly, it is increasingly clear that measuring biomarkers may improve the definition of cerebrovascular risk profile in patients with Type 2 diabetes mellitus.

Effect of omega-3 fish oil on cardiovascular risk in diabetes

PURPOSE

Diabetes and cardiovascular disease are major public health concerns worldwide and are leading causes of morbidity and mortality. People with type 2 diabetes are at an increased risk for cardiovascular disease. Diet has a substantial affect on the progression of many diseases, including diabetes, cardiovascular disease, osteoporosis, and arthritis. Omega-3 polyunsaturated fatty acids (long-chain polyunsaturated fatty acids [LC-PUFA]) have long been attributed to the maintenance of health and may be of benefit in reducing cardiovascular risk. The purpose of this review is to investigate the possible roles of omega-3 in reducing cardiovascular risk in patients with diabetes.

METHODS

A literature search was conducted from the Medline, EBSCO, and EMBASE databases. Articles that addressed diabetes, cardiovascular disease, or omega-3 were included.

RESULTS

Reviews and studies reported an association with fish and omega-3 LC-PUFA consumption and decreased total cardiovascular mortality (approximately 15%-19%), along with decreased platelet activation and aggregation, improved lipid profiles, including reduction of triglycerides and very low-density lipoprotein (VLDL), decreased inflammation, and lowered blood pressure.

CONCLUSION

Diets higher in fish and omega-3 LC-PUFA may reduce cardiovascular risk in diabetes by inhibiting platelet aggregation, improving lipid profiles, and reducing cardiovascular mortality. Fish and omega-3 LC-PUFA can be recommended to people with diabetes and included into a diabetes management program.

Clinical application of blood biomarkers in cerebrovascular disease

Identifying a biomarker or panel of biomarkers of cerebral ischemia would have a major impact on the care of stroke patients by facilitating early management decisions and individualization of care. Biochemical surrogates of cerebral ischemia might also play an important role by identifying relevant pathways for novel therapeutic strategies and by facilitating early clinical trials in cerebrovascular disease. Serum biomarkers related to pathways of hemostasis, oxidation and inflammation, or alterations in glial and neuronal proteins, have been identified but none have been recommended for routine clinical use. This review describes the most promising biomarkers of cerebrovascular disease and the context and limitations in which they have been studied.

Proteome of platelets in patients with coronary artery disease

OBJECTIVE

This study aimed at investigating the protein patterns of platelets from patients with stable or acute coronary atherosclerosis (CAD), in which platelets play a key role.

MATERIALS AND METHODS

A proteomic approach was adopted to investigate specific protein patterns in platelets of patients with non-ST elevation acute coronary syndrome, stable angina, or of subjects with no history of CAD.

RESULTS

Six differentially expressed proteins were identified: two involved in energy metabolism (2-oxoglutarate dehydrogenase [OGDH], and lactate dehydrogenase [LDH]); three were associated with cytoskeleton-based processes (gamma-actin, coronin 1B, and pleckstrin); and one involved in protein degradation (proteasome subunit type 8). Expression levels of OGDH and a cleaved form of gamma-actin were significantly higher in the platelets of patients than in controls, whereas that of LDH was higher only in the platelets of patients with acute coronary disease. The increases in protein expression of OGDH and LDH are paralleled by changes in their functional activities. Coronin and proteasome subunit type 8 were less expressed in the platelets of patients, as were the basic isoforms of pleckstrin.

CONCLUSION

The platelet proteome is altered in CAD patients with stable or acute coronary syndrome possibly because of the ongoing atherosclerotic process. The identified protein changes not previously connected with CAD were an increase in the energy metabolism enzymes and alterations in the proteins associated with cytoskeleton-based processes, both of which indicate platelet activation.

Identification of quantitative trait loci for fibrin clot phenotypes: the EuroCLOT study

OBJECTIVE

Fibrin makes up the structural basis of an occlusive arterial thrombus, and variability in fibrin phenotype relates to cardiovascular risk. The aims of the current study from the EU consortium EuroCLOT were to (1) determine the heritability of fibrin phenotypes and (2) identify QTLs associated with fibrin phenotypes.

METHODS AND RESULTS

447 dizygotic (DZ) and 460 monozygotic (MZ) pairs of healthy UK white female twins and 199 DZ twin pairs from Denmark were studied. D-dimer, an indicator of fibrin turnover, was measured by ELISA and measures of clot formation, morphology, and lysis were determined by turbidimetric assays. Heritability estimates and genome-wide linkage analysis were performed. Estimates of heritability for d-dimer and turbidometric variables were in the range 17% to 46%, with highest levels for maximal absorbance which provides an estimate of clot density. Genome-wide linkage analysis revealed 6 significant regions with LOD >3 on 5 chromosomes (5, 6, 9, 16, and 17).

CONCLUSIONS

The results indicate a significant genetic contribution to variability in fibrin phenotypes and highlight regions in the human genome which warrant further investigation in relation to ischemic cardiovascular disorders and their therapy.