Does the genotype predict the phenotype? Evaluations of the hemostatic proteome

Modifiers of clinical phenotype in severe congenital hemophilia

Patients with inherited hemophilia A and B usually exhibit a bleeding tendency of a severity proportional to the degree of plasmatic deficiency of the coagulant activity of factor VIII (FVIII:C) and factor IX (FIX:C). Although patients with severe hemophilia (i.e., with FVIII:C and FIX:C levels <1IU/dL) are generally those with the most severe bleeding phenotype, it is common experience that a variable proportion of them experiences a milder bleeding tendency. In this review, we summarize the current knowledge on the possible mechanisms at the basis of the phenotypic heterogeneity of severe hemophilia, focusing in particular on the role of FVIII/FIX gene mutations and thrombophilic polymorphisms. Finally, the possible therapeutic implications of such modifiers will be analyzed.

Computational modelling of clot development in patient-specific cerebral aneurysm cases

ESSENTIALS: Clotting in cerebral aneurysms is a process that can either stabilize the aneurysm or lead to rupture. A patient-specific computational model capable of predicting cerebral aneurysm thrombosis is presented. The different clotting outcomes highlight the importance of personalization of treatment. Once validated, the model can be used to tailor treatment and to clarify clotting processes in aneurysms.

BACKGROUND

In cerebral aneurysms, clotting can either stabilize the aneurysm sac via aneurysm occlusion, or it can have a detrimental effect by giving rise to embolic occlusion.

OBJECTIVE

The work presented in this study details the development of an in silico model that combines all the salient, clinically relevant features of cerebral aneurysm clotting. A comprehensive computational model of clotting that accounts for biochemical complexity coupled with three-dimensional hemodynamics in image-derived patient aneurysms and in the presence of virtually implanted interventional devices is presented.

METHODS

The model is developed and presented in two stages. First, a two-dimensional computational model of clotting is presented for an idealized geometry. This enables verification of the methods with existing, physiological data before the pathological state is considered. This model is used to compare the results predicted by two different underlying biochemical cascades. The two-dimensional model is then extended to image-derived, three-dimensional aneurysmal topologies by incorporating level set methods, demonstrating the potential use of this model.

RESULTS AND CONCLUSION

As a proof of concept, comparisons are then made between treated and untreated aneurysms. The prediction of different clotting outcomes for different patients demonstrates that with further development, refinement and validation, this methodology could be used for patient-specific interventional planning.

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.

In vitro effects of recombinant activated factor VII on thrombin generation and coagulation following inhibition of platelet procoagulant activity by prasugrel

INTRODUCTION

Prasugrel is a thienopyridyl P2Y12 antagonist with potent antiplatelet effects. At present, little is known about its effects on thrombin generation or what strategies may emergently reverse its anticoagulant effects. In the current study we evaluated whether recombinant activated factor VII may reverse prasugrel induced effects and increase thrombin generation in an in vitro model.

METHODS

The effect of prasugrel active metabolite, PAM (R-138727), was evaluated on platelet aggregation, thrombin generation, and rotational thromboelastometry parameters using blood from 20 healthy volunteers. Additionally, we evaluated the effects of adenosine diphosphate (ADP) and recombinant activated factor VII on restoring these parameters towards baseline values.

RESULTS

PAM reduced maximum platelet aggregation and led to platelet disaggregation. It also decreased peak thrombin, increased lag time, and increased time to peak thrombin. Treatment with recombinant activated factor VII restored all three parameters of thrombin generation towards baseline. ADP decreased lag time and time to peak thrombin, but had no effect on peak thrombin. When recombinant activated factor VII and ADP were combined they had a greater effect on thrombin parameters than either drug alone. PAM also increased thromboelastometric clotting time and clot formation time, but had no effect on maximum clot firmness. Treatment with either recombinant activated factor VII or ADP restored these values towards baseline.

CONCLUSIONS

Recombinant activated factor VII restores thrombin generation in the presence of PAM. In patients taking prasugrel with life-threatening refractory bleeding it has the potential to be a useful therapeutic approach. Additional clinical studies are needed to validate our findings.

Monitoring rFVIII prophylaxis dosing using global haemostasis assays

Secondary factor VIII (FVIII) prophylaxis converts severe haemophiliacs (FVIII:C < 1 IU dL(-1)) to a moderate phenotype (FVIII:C ≥ 1 IU dL(-1)), however, plasma FVIII:C is a poor predictor of bleeding risk. This study used thromboelastography (TEG) and thrombin generation assay (TGA) to quantify coagulation across a 48 h rFVIII prophylaxis period. 10 severe haemophiliacs with varying clinical bleeding phenotypes received their standard rFVIII prophylaxis dose and blood samples were obtained over 48 h. Measured parameters included FVIII:C, TEG and TGA at each time point. FVIII:C pharmacokinetics (PK) and correlation between global assay parameters was performed. The FVIII:C PK parameters were consistent with previous literature. There was significant correlation between FVIII:C and TEG R-time and aPTT (both P < 0.001). Significant correlations existed between FVIII:C and TGA peak, ETP and velocity parameters (all P < 0.001). At 24 h the TEG parameters were sub-therapeutic despite median FVIII:C of 13.0 IU dL(-1). TGA was sensitive to FVIII:C below 1 IU dL(-1). Those with the severest bleeding phenotype had the lowest TGA parameters. There was significant correlation between FVIII:C and TEG and TGA. TEG lost sensitivity at 48 h, but not TGA. Prospective studies are needed to determine whether these data can be used to design individualized rFVIII prophylaxis regimens.

Proteomics-based investigations of animal models of disease

Cells contain a large yet, constant genome, which contains all the coding information necessary to sustain cellular physiology. However, proteins are the end products of genes, and hence dictate the phenotype of cells and tissues. Therefore, proteomics can provide key information for the elucidation of physiological and pathophysiological mechanisms by identifying the protein profile from cells and tissues. The relatively novel techniques used for the study of proteomics thus have the potential to improve diagnostic, prognostic, as well as therapeutic avenues. In this review, we first discuss the benefits of animal models over the use of human samples for the proteomic analysis of human disease. Next, we aim to demonstrate the potential of proteomics in the elucidation of disease mechanisms that may not be possible by other conventional technologies. Following this, we describe the use of proteomics for the analysis of PTM and protein interactions in animal models and their relevance to the study of human disease. Finally, we discuss the development of clinical biomarkers for the early diagnosis of disease via proteomic analysis of animal models. We also discuss the development of standard proteomes and relate how this data will benefit future proteomic research. A comprehensive review of all animal models used in conjunction with proteomics is beyond the scope of this manuscript. Therefore, we aimed to cover a large breadth of topics, which together, demonstrate the potential of proteomics as a powerful tool in biomedical research.

Computational analysis of intersubject variability and thrombin generation in dilutional coagulopathy

BACKGROUND

Blood dilution is a frequent complication of massive transfusion during trauma and surgery. This article investigates the quantitative effects of blood plasma dilution on thrombin generation in the context of intersubject variability.

STUDY DESIGN AND METHODS

A thoroughly validated computational model was used to simulate thrombin generation curves for 472 healthy subjects in the Leiden Thrombophilia Study. Individual thrombin curves were calculated for undiluted blood and for different dilution scenarios. For every such curve, five standard quantitative parameters of thrombin generation were calculated and analyzed.

RESULTS

Thrombin generation parameters in diluted blood plasma displayed significant intersubject variability (with a coefficient of variation up to approx. 28%). Nevertheless, dilutional effects in the majority (or all) of the subjects in the study group were characterized by persistent patterns. In particular, the largest dilution-induced change typically occurred in the maximum slope (MS) of the thrombin curve, followed by a change in thrombin peak height (PH), whereas the smallest change often occurred in the area under the curve. The identified patterns demonstrated considerable robustness to variations in dilution scenario and tissue factor concentration.

CONCLUSION

Dilutional effects on thrombin generation in a human population can be predicted from trends identified for the "average" subject and then refined by performing an analysis of actual subjects in the study group. The MS and PH are dilution indicators that are both sensitive and reliable across a large subject group and could potentially be used as disease markers in the diagnosis of coagulopathic conditions.

Thrombin generation testing in haemophilia comprehensive care centres

SUMMARY

Haemophilia comprehensive care centres (HCCC) were first created more than 50 years ago. Their first objective was educating the patient and healthcare professionals in the management of bleeding. Today HCCCs are centres of excellence with multidisciplinary specialists, which continue to provide essential services that are continually reassessed in light of new scientific information. In addition, HCCCs make significant research contributions by studying new methods to improve the well-being of patients with haemophilia. Laboratory expertise is one of the central pillars of HCCCs with a direct impact on diagnosis and management of the haemophilia disease. Vast efforts have been made for the standardization of factor VIII (FVIII) and FIX measurements and inhibitor detection. Molecular biology has improved diagnostics and made it possible to develop new, more secure FVIII and FIX concentrates for replacement therapy. However, phenotyping of each haemophilia patient with an accurate prediction of the individual bleeding risk and also the individual response of patients to antihaemophilic treatment still remains a challenge. In the last 5 years, an expanding interest of haematologists for thrombin generation testing (TGT) reflects the need for new laboratory tools able to evaluate the overall coagulating capacity of patients. This study will review unmet laboratory needs in haemophilia and the potential applications of TGT in the management of haemophiliacs. Furthermore, technical and standardization issues of the method will be discussed.

"Proteotyping": population proteomics of human leukocytes using top down mass spectrometry

Characterizing combinations of coding polymorphisms (cSNPs), alternative splicing and post-translational modifications (PTMs) on a single protein by standard peptide-based proteomics is challenging owing to <100% sequence coverage and the uncoupling effect of proteolysis on such variations >10-20 residues apart. Because top down MS measures the whole protein, combinations of all the variations affecting primary sequence can be detected as they occur in combination. The protein form generated by all types of variation is here termed the "proteotype", akin to a haplotype at the DNA level. Analysis of proteins from human primary leukocytes harvested from leukoreduction filters using a dual on-line/off-line top down MS strategy produced >600 unique intact masses, 133 of which were identified from 67 unique genes. Utilizing a two-dimensional platform, termed multidimensional protein characterization by automated top down (MudCAT), 108 of the above protein forms were subsequently identified in the absence of MS/MS in 4 days. Additionally, MudCAT enables the quantitation of allele ratios for heterozygotes and PTM occupancies for phosphorylated species. The diversity of the human proteome is embodied in the fact that 32 of the identified proteins harbored cSNPs, PTMs, or were detected as proteolysis products. Among the information were three partially phosphorylated proteins and three proteins heterozygous at known cSNP loci, with evidence for non-1:1 expression ratios obtained for different alleles.

Thrombin generation: a comparison of assays using platelet-poor and -rich plasma and whole blood samples from healthy controls and patients with a history of venous thromboembolism

We have developed a whole blood thrombin generation (TG) assay whereby TG is initiated with a low-tissue factor concentration and monitored using a fluorogenic thrombin substrate. Significantly higher values were found in blood samples from 50 patients with a history of venous thromboembolism (VTE) compared with 31 healthy controls (HC), for peak height (P = 0.0034) and endogenous thrombin potential (ETP) (P = 0.0027). Results from 31 VTE patients and the 31 controls in the absence of corn trypsin inhibitor (CTI) showed significantly higher values in the VTE group for peak height (P = 0.0013) and ETP (P = 0.002). In the presence of CTI, significantly higher values were only seen in ETP (P = 0.024). No significant increases in TG were found using platelet poor (PPP) or -rich (PRP) plasma with or without CTI. The whole blood TG assay in the absence or presence of CTI showed a higher proportion (25/50 and 12/31, respectively) of raised peak height and/or ETP values than plasma assays (PPP 9/50 and 5/31 respectively and PRP 13/50 and 6/31, respectively). Our results show the whole blood TG assay is more sensitive for determining the increases in TG in patients with a history of VTE than PPP and PRP TG assays.

Measurement of global haemostasis in severe haemophilia A following factor VIII infusion

Patients with haemophilia requires different amounts of FVIII to prevent and treat bleeds. We hypothesise that this is because FVIII has variable effects on individual patients' global haemostasis. Twelve patients with severe haemophilia A were infused with 50 IU/kg FVIII and thrombin generation in platelet rich (PRP) and platelet poor plasma (PPP) and velocity of changing clot elasticity were measured preinfusion and at nine subsequent time points over 72 h. Despite a close correlation between median FVIII and median initial rate of thrombin generation (R(2) 0.94), endogenous thrombin potential (ETP; R(2) 0.94) and peak thrombin (R(2) 0.91) in PPP, there was wide inter-patient variability at each time point. There was, however, a highly predictable intra-patient relationship between FVIII level and thrombin generation. Inter-patient variability was due to both differences in FVIII levels and the variable effect FVIII had on an individuals' thrombin generation. The utility of PRP was limited because, at low-FVIII levels, only rate of thrombin generation was measurable. At low-FVIII concentrations, the rate of thrombin generation in PPP was the most useful test whilst at higher levels ETP and peak thrombin could also be used.

Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications

Recent advances in proteomics technologies provide tremendous opportunities for biomarker-related clinical applications; however, the distinctive characteristics of human biofluids such as the high dynamic range in protein abundances and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS-based proteomics profiling and its applications in clinical proteomics as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/ml levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomics profiling platform suitable for efficient clinical applications can be routinely implemented.

Platelet-dependent thrombography: a method for diagnostic laboratories

The thrombin-platelet feedback loop was examined at low concentration tissue factor using calibrated automated thrombography in combination with the elimination of contact factor activation by corn trypsin inhibitor. The results indicated that, when contact factor activation was eliminated, the thrombin-platelet feedback loop was a major determinant of thrombin generating capacity and that platelets had a greater role in regulating the propagation of thrombin generation than its initiation. This method has potential application to the measurement of platelet-dependent thrombin generation in clinical diagnostic laboratories and hence the investigation of patients with apparent hypo- or hypercoagulable phenotypes.

Models of blood coagulation

Our research aims to provide quantitatively transparent, biologically realistic descriptions of the processes involved in hemostasis which will permit predictions of the behavior of the coagulation system in normal and pathologic states. We use four models of coagulation: (1) numerical approximations of the tissue factor (Tf) pathway of thrombin generation based upon mechanism and dynamics; (2) Tf activation of the "blood coagulation proteome" from isolated cells and proteins; (3) Tf activated contact pathway inhibited whole blood in vitro; and (4) blood shed from standardized microvascular wounds in vivo. The results from these models are integrated in interactive assessments aimed at achieving convergence of biochemical rigor and biological authenticity. Microvascular injury is the most biologically secure but least accessible to mechanistic study. Numerical models while quantitatively transparent are biologically limited. By the integrated analyses of all four models, we establish observations which require inclusion or discovery of new parameters to achieve mechanistically interpretable biological reality. Discoveries made in this fashion have included thrombin's role in the initiation phase, TFPI/ATIII/APC synergy interactions, rfVIIa in fVII deficiency, the roles of fVIII and fIX in the Tf reaction, and the cleavage of fIX by fXa membrane. Ideally, our results will provide descriptions which predict the behavior of the biological blood coagulation system under normal and pathologic conditions.

Thrombin generation profiles in deep venous thrombosis

BACKGROUND

Reliable markers and methods to predict risk for thrombosis are essential to clinical management.

OBJECTIVE

Using an integrated approach that defines an individual's comprehensive coagulation phenotype might prove valuable in identifying individuals at risk for experiencing a thrombotic event.

METHODS

Using a numerical simulation model, we generated tissue factor (TF) initiated thrombin curves using coagulation factor levels from the Leiden Thrombophilia Study population and evaluated thrombotic risk, by sex, age, smoking, alcohol consumption, body mass index (BMI) and oral contraceptive (OC) use. We quantitated the initiation, propagation and termination phases of each individuals' comprehensive TF-initiated thrombin generation curve by the parameters: time to 10 nm of thrombin, maximum time, level and rate (MaxR) of thrombin generated and total thrombin.

RESULTS

The greatest risk association was obtained using MaxR; with a 2.6-fold increased risk at MaxR exceeding the 90th percentile. The odds ratio (OR) for MaxR was 3.9 in men, 2.1 in women, and 2.9 in women on OCs. The association of risk with thrombin generation did not differ by age (OR:2.8 OR:2.5), BMI (OR:2.9 OR:2.3) or alcohol use. In both numerical simulations and empirical synthetic plasma, OC use created extreme shifts in thrombin generation in both control women and women with a prior thrombosis, with a larger shift in thrombin generation in control women. This suggests an interaction of OC use with underlying prothrombotic abnormalities.

CONCLUSIONS

Thrombin generation based upon the individual's blood composition is associated with the risk for thrombosis and may be useful as a predictive marker for evaluating thrombosis on an individual basis.

Recent advances in blood-related proteomics

Blood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.

The measurement and application of thrombin generation

It is the capacity to generate thrombin, and the enzymatic work that thrombin does, that determines blood coagulability. Therefore, measurement of the enzymatic work potential of thrombin provides a method for quantifying the composite effect of the multiple factors that determine coagulation capacity. The application of measurement of thrombin generation to clinical decision making has been hampered by numerous technical difficulties and pitfalls, many of which have now been overcome. Technical advances now permit rapid, reproducible measurement. A review of clinical studies performed to date indicates the need to appreciate the precise methodology used in each case and the need to consider standardisation in future studies. Applying thrombin generation measurement to clinical decision making will require up-to-date estimates of risks relating to the disorder and the intended therapeutic intervention. Ultimately management studies will be required if the clinical utility of measurement of thrombin generation is to be proven.