Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories

Cardiovascular disease (CVD) and venous thromboembolism (VTE) figure among the main causes of morbidity and mortality in modern societies. Although associated with distinct pathogenic mechanisms, epidemiological, experimental and clinical trial data suggest that the mechanisms responsible for arterial and venous thrombosis are at least partially overlapped. Herein we aimed to explore shared and discordant pathways involved in the pathogenesis of VTE and CVD at the transcriptomic level and to validate the results in independent cohorts. Five public datasets of gene expression data from VTE and CVD (myocardial infarction, peripheral arterial occlusive disease and stroke) patients were analyzed using an integrative bioinformatic strategy. A machine/statistical learning method was used to derive classifiers for the discrimination of VTE and CVD, and tested in independent datasets. Two sets of genes that were commonly (n = 472) or divergently (n = 124) expressed in CVD and VTE were identified. Genes and pathways associated with innate immune function were over-represented in both conditions, along with pathways associated with complement and hemostasis. Pathways associated with neutrophil activation and with IL-1 signaling were also enriched in CVD compared to VTE. The gene expression signature of VTE more closely resembled the pattern of cardioembolic stroke than the patterns of acute myocardial infarction, ischemic stroke and peripheral arterial occlusive disease. Classifiers derived from these gene lists accurately discriminated patients with VTE and CVD from independent cohorts. In conclusion, our results add a new set of data at the transcriptomic level for future studies between arterial and venous thrombosis.

SLC44A2 deficient mice have a reduced response in stenosis but not in hypercoagulability driven venous thrombosis

BACKGROUND

Genome wide association studies (GWAS) identified SLC44A2 as a novel susceptibility gene for venous thrombosis (VT) and previous work established that SLC44A2 contributed to clot formation upon vascular injury.

OBJECTIVE

To further investigate the role of SLC44A2 in VT by utilizing SLC44A2 deficient mice (Slc44a2-/- ) in two representative disease models.

METHODS

Mice were included in a hypercoagulability model driven by siRNA-mediated hepatic gene silencing of anticoagulants Serpinc1 (antithrombin) and Proc (protein C) and a flow restriction (stenosis) model induced by partial ligation of the inferior vena cava.

RESULTS

In the hypercoagulability model, no effect in onset was observed in Slc44a2-/- animals; however, a drop in plasma fibrinogen and von Willebrand factor coinciding with an increase in blood neutrophils was recorded. In the neutrophil dependent stenosis model after 48 hours, Slc44a2-/- mice had significantly smaller thrombi both in length and weight with less platelet accumulation as a percentage of the total thrombus area. During the initiation of thrombosis at 6 hours post-stenosis, Slc44a2-/- mice also had smaller thrombi both in length and weight, with circulating platelets remaining elevated in Slc44a2-/- animals. Platelet activation and aggregation under both static- and venous and arterial shear conditions were normal for blood from Slc44a2-/- mice.

CONCLUSIONS

These studies corroborate the original GWAS findings and establish a contributing role for SLC44A2 during the initiation of VT, with indications that this may be related to platelet-neutrophil interaction. The precise mechanism however remains elusive and warrants further investigation.

Activated αIIbβ3 on platelets mediates flow-dependent NETosis via SLC44A2

Platelet-neutrophil interactions are important for innate immunity, but also contribute to the pathogenesis of deep vein thrombosis, myocardial infarction and stroke. Here we report that, under flow, von Willebrand factor/glycoprotein Ibα-dependent platelet 'priming' induces integrin αIIbβ3 activation that, in turn, mediates neutrophil and T-cell binding. Binding of platelet αIIbβ3 to SLC44A2 on neutrophils leads to mechanosensitive-dependent production of highly prothrombotic neutrophil extracellular traps. A polymorphism in SLC44A2 (rs2288904-A) present in 22% of the population causes an R154Q substitution in an extracellular loop of SLC44A2 that is protective against venous thrombosis results in severely impaired binding to both activated αIIbβ3 and VWF-primed platelets. This was confirmed using neutrophils homozygous for the SLC44A2 R154Q polymorphism. Taken together, these data reveal a previously unreported mode of platelet-neutrophil crosstalk, mechanosensitive NET production, and provide mechanistic insight into the protective effect of the SLC44A2 rs2288904-A polymorphism in venous thrombosis.

Resistin Promotes Thrombosis in Rats with Deep Vein Thrombosis via Up-Regulating MMP-2, MMP-9, and PAI-1

BACKGROUND

To explore the role of resistin (RE) on deep vein thrombosis (DVT) and the molecular mechanism.

METHODS

ELISA assay was used to determine the concentration of RE, MMP-2, MMP-9, and PAI-1 in serum of DVT patients and controls. Rats were randomly divided into 4 groups: control, DVT, DVT + RE, and DVT + RE + SB203580 group. HE staining was used to observe the intravascular situation and thrombosis in the 4 groups. The relative mRNA levels and protein expression of RE, MMP-2, MMP-9, and PAI-1 in the 4 groups were determined by RT-PCR and western blotting.

RESULTS

The concentration of RE, MMP-2, MMP-9, and PAI-1 in serum from DVT patients was significantly higher than that in controls. RE promoted thrombosis in rats with DVT, while SB203580 inhibited the promotion of RE on thrombosis. RE up-regulated the expression of MMP-2, MMP-9, and PAI-1 in DVT rat models. Introduction of SB203580 inhibited the expression of RE, which then abolished the up-regulation role of RE on the expression of MMP-2, MMP-9, and PAI-1.

CONCLUSIONS

RE promoted thrombosis in DVT rat models by increasing the expression of MMP-2, MMP-9, and PAI-1.

Hereditary Antithrombin Deficiency Presenting with Deep Venous Thrombosis During the Second Pregnancy

A 37-year-old woman developed deep venous thrombosis (DVT) of the left lower extremity at 8 weeks of gestation during her second pregnancy. There was no personal or family history of thrombosis. She received intravenous heparin, but heparin resistance was noted. The plasma antithrombin activity decreased to 45% in the acute phase, and it remained low postpartum. Her mother also had low plasma antithrombin activity (46%), and genetic testing revealed a heterozygous SERPINC1 mutation. Even without a family history of thrombosis, we should suspect hereditary antithrombin deficiency in patients with initial DVT and perform thorough investigation.

Prediction of recurrent venous thrombosis in all patients with a first venous thrombotic event: The Leiden Thrombosis Recurrence Risk Prediction model (L-TRRiP)

BACKGROUND

Recurrent venous thromboembolism (VTE) is common. Current guidelines suggest that patients with unprovoked VTE should continue anticoagulants unless they have a high bleeding risk, whereas all others can stop. Prediction models may refine this dichotomous distinction, but existing models apply only to patients with unprovoked first thrombosis. We aimed to develop a prediction model for all patients with first VTE, either provoked or unprovoked.

METHODS AND FINDINGS

Data were used from two population-based cohorts of patients with first VTE from the Netherlands (Multiple Environment and Genetic Assessment of Risk Factors for Venous Thrombosis [MEGA] follow-up study, performed from 1994 to 2009; model derivation; n = 3,750) and from Norway (Tromsø study, performed from 1999 to 2016; model validation; n = 663). Four versions of a VTE prediction model were developed: model A (clinical, laboratory, and genetic variables), model B (clinical variables and fewer laboratory markers), model C (clinical and genetic factors), and model D (clinical variables only). The outcome measure was recurrent VTE. To determine the discriminatory power, Harrell's C-statistic was calculated. A prognostic score was assessed for each patient. Kaplan-Meier plots for the observed recurrence risks were created in quintiles of the prognostic scores. For each patient, the 2-year predicted recurrence risk was calculated. Models C and D were validated in the Tromsø study. During 19,201 person-years of follow-up (median duration 5.7 years) in the MEGA study, 507 recurrences occurred. Model A had the highest predictive capability, with a C-statistic of 0.73 (95% CI 0.71-0.76). The discriminative performance was somewhat lower in the other models, with C-statistics of 0.72 for model B, 0.70 for model C, and 0.69 for model D. Internal validation showed a minimal degree of optimism bias. Models C and D were externally validated, with C-statistics of 0.64 (95% CI 0.62-0.66) and 0.65 (95% CI 0.63-0.66), respectively. According to model C, in 2,592 patients with provoked first events, 367 (15%) patients had a predicted 2-year risk of >10%, whereas in 1,082 patients whose first event was unprovoked, 484 (45%) had a predicted 2-year risk of <10%. A limitation of both cohorts is that laboratory measurements were missing in a substantial proportion of patients, which therefore were imputed.

CONCLUSIONS

The prediction model we propose applies to patients with provoked or unprovoked first VTE-except for patients with (a history of) cancer-allows refined risk stratification, and is easily usable. For optimal individualized treatment, a management study in which bleeding risks are also taken into account is necessary.

Danhong Huayu Koufuye prevents venous thrombosis through antiinflammation via Sirtuin 1/NF-κB signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Danhong Huayu Koufuye (DHK), a compound traditional Chinese medicine, is composed of Salvia miltiorrhiza radix (Salvia miltiorrhiza Bge.), Angelicae Sinensis radix (Angelicae Sinensis (Oliv.) Diels.), Chuanxiong rhizoma (Ligusticum chuanxiong Hort.), Persicae semen (Prunus persica (L.) Batsch), Carthami flos (Carthamus tinctorius L.), Bupleuri radix (Bupleurum chinense DC.) and Aurantii fructus (Citrus aurantium L.). DHK prevents deep vein thrombosis (DVT) through antiinflammation. However, the antiinflammatory mechanism of DHK is still unknown.

OBJECTIVE

The aim of this study was to evaluate whether DHK prevented venous thrombosis through antiinflammation via Sirtuin 1 (SIRT1)/NF-κB signaling pathway.

METHODS

Inferior vena cava (IVC) stenosis-induced DVT rat model was established. Rats were administered with DHK (1.6, 3.2 or 6.4 mL/kg/d, p.o.), heparin (200 U/kg/d, i.v.), clopidogrel (25 mg/kg/d, p.o.), resveratrol (50 mg/kg/d, p.o.) or vehicle (p.o.) once daily for two days. Blood coagulation, blood fibrinolysis, blood viscosity, blood cell counts and platelet activity were evaluated. Serum levels of inflammatory cytokines were analyzed by enzyme-linked immunosorbent assay. Pathological changes were observed by hematoxylin-eosin (HE) staining. Protein expressions in thrombosed IVCs were evaluated by Western blot and/or immunofluorescence analyses. SIRT1 mRNA expression was analyzed by real-time quantitative polymerase chain reaction. Besides, SIRT1-specific inhibitor EX527 was pretreated to confirm the role of SIRT1/NF-κB signaling pathway in the antithrombotic effect of DHK.

RESULTS

DHK remarkably prevented DVT. DHK had no effects on blood coagulation, blood fibrinolysis, blood viscosity, blood cell counts or platelet activity. But DHK significantly up-regulated protein and mRNA expressions of SIRT1, and reduced leukocytes infiltration into thrombus and vein wall, serum levels of inflammatory cytokines, and protein expressions of acetylated p65 (Ace-p65), phosphorylated p65 (p-p65) and tissue factor (TF). Moreover, the antithrombotic effect of DHK was significantly abolished by EX527.

CONCLUSION

DHK may prevent DVT by inhibiting inflammation via SIRT1/NF-κB signaling pathway.

Two Novel Mutations Cause Hereditary Antithrombin Deficiency in a Chinese Family

OBJECTIVE

To study the molecular basis of hereditary antithrombin (AT) deficiency in a Chinese family. It will help us understand the pathogenesis of this type of disease.

METHOD

AT activity (AT:A) and the AT antigen (AT:Ag) level were tested by chromogenic substrate and immunoturbidimetry, respectively. To identify the novel mutations, SERPINC1 gene sequencing was carried out. The possible impact of the mutations was analyzed by model and bioinformatic analyses.

RESULTS

AT:A and the AT:Ag level of the proband were 43% and 113 mg/L (normal range: 98-119% and 250-360 mg/L), respectively. Sequencing analysis revealed compound heterozygous mutations, including a frameshift mutation (c.318_319insT) resulting in Asn75stop and a missense mutation (c.922G>T) resulting in Gly276Cys. The bioinformatic and model analyses indicated that these mutations may disrupt the function and structure of the AT protein.

CONCLUSION

We detected 2 novel heterozygous mutations (c.318_319insT and c.922G>T) in the proband, and these were associated with decreased AT:A.

The association of genetic variants in the cholesteryl ester transfer protein gene with hemostatic factors and a first venous thrombosis

BACKGROUND

Cholesteryl ester transfer protein (CETP) plays an important role in lipoprotein metabolism. Previous studies have suggested that the CETP TaqI B1/B2 allele is associated with the risk of venous thrombosis (VT).

AIM

To investigate the associations between genetically determined CETP concentrations and 22 hemostatic factors in healthy individuals, and the risk of a first VT event, in a large VT case-control study.

METHODS

Analyses were performed in the Multiple Environmental and Genetic Assessment of Risk Factors for Venous Thrombosis (MEGA) case-control study. CETP unweighted/weighted genetic risk scores (GRSs) were derived from three single-nucleotide polymorphisms that were identified from a recent genome-wide association study on serum CETP concentrations. The associations between CETP GRSs and 22 hemostatic factors (procoagulant/anticoagulant and fibrinolytic factors) were assessed by linear regression from an additive model in controls (n = 2813). The associations between CETP GRSs and the risk of a first VT were assessed by logistic regression analyses in 3950 VT cases and 4765 controls.

RESULTS

In the controls (median age, 49 years; 53% women), both unweighted and weighted GRSs showed that factor VII activity was negatively associated with the genetically determined CETP concentration (weighted GRS β -3.08 IU/dL per μg/mL genetically determined CETP, 95% confidence interval -5.73 to -0.42). No association was observed with the risk of a first VT.

CONCLUSIONS

Genetically determined CETP concentrations only showed a weak negative association with factor VII activity. However, this did not lead to an association with the risk of a first VT.

Tspan18 is a novel regulator of the Ca2+ channel Orai1 and von Willebrand factor release in endothelial cells

Ca2+ entry via Orai1 store-operated Ca2+ channels in the plasma membrane is critical to cell function, and Orai1 loss causes severe immunodeficiency and developmental defects. The tetraspanins are a superfamily of transmembrane proteins that interact with specific 'partner proteins' and regulate their trafficking and clustering. The aim of this study was to functionally characterize tetraspanin Tspan18. We show that Tspan18 is expressed by endothelial cells at several-fold higher levels than most other cell types analyzed. Tspan18-knockdown primary human umbilical vein endothelial cells have 55-70% decreased Ca2+ mobilization upon stimulation with the inflammatory mediators thrombin or histamine, similar to Orai1-knockdown. Tspan18 interacts with Orai1, and Orai1 cell surface localization is reduced by 70% in Tspan18-knockdown endothelial cells. Tspan18 overexpression in lymphocyte model cell lines induces 20-fold activation of Ca2+ -responsive nuclear factor of activated T cell (NFAT) signaling, in an Orai1-dependent manner. Tspan18-knockout mice are viable. They lose on average 6-fold more blood in a tail-bleed assay. This is due to Tspan18 deficiency in non-hematopoietic cells, as assessed using chimeric mice. Tspan18-knockout mice have 60% reduced thrombus size in a deep vein thrombosis model, and 50% reduced platelet deposition in the microcirculation following myocardial ischemia-reperfusion injury. Histamine- or thrombin-induced von Willebrand factor release from endothelial cells is reduced by 90% following Tspan18-knockdown, and histamine-induced increase of plasma von Willebrand factor is reduced by 45% in Tspan18-knockout mice. These findings identify Tspan18 as a novel regulator of endothelial cell Orai1/Ca2+ signaling and von Willebrand factor release in response to inflammatory stimuli.

Vascular Behçet's syndrome: an update

Behçet's syndrome (BS) is a complex vasculitis, characterised by peculiar histological, pathogenetic and clinical features. Superficial venous thrombosis (SVT) and deep vein thrombosis (DVT) are the most frequent vascular involvements, affecting altogether 15-40% of BS patients. Atypical thrombosis is also an important clinical feature of BS, involving the vascular districts of the inferior and superior vena cava, suprahepatic veins with Budd-Chiari syndrome, portal vein, cerebral sinuses and right ventricle. On the other hand, arterial involvement, although affecting only 3-5% of patients, represents a unique feature of BS, with aneurysms potentially affecting peripheral, visceral and pulmonary arteries. Vascular events in BS are promoted by inflammation, with neutrophils playing a key role in the pathogenesis of thrombotic events; in turn, coagulative components such as fibrinogen, thrombin, factor Xa and factor VIIa amplify the inflammatory cascade. Understanding the contribution of inflammatory and coagulation components in the pathogenesis of BS vascular events is crucial to define the most effective therapeutic strategy. Control of vascular thrombosis is achieved with immunosuppressants drugs rather than anticoagulants. In particular, use of azathioprine and cyclosporine in association with low-dose corticosteroids should be considered in DVT and SVT cases, while treatment with cyclophosphamide together with anti-TNF-α agents can be effectively used in arterial involvement. More recently, the anti-TNF-α drugs have also been reported as a valid alternative for the treatment also of venous events, especially DVT. An exception to the use of anticoagulant in BS could be represented by cerebral veins thrombosis. In this review, we will depict the main characteristics of the vascular involvement in BS, briefly describing histological and pathogenetic features, while focusing on the clinical and therapeutical approaches of the vascular manifestations of BS.

OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis

Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs' detection and quantification still remain a challenge as they can undergo different posttranscriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).

Association of TFPI polymorphisms rs8176592, rs10931292, and rs10153820 with venous thrombosis: A meta-analysis

BACKGROUND

Tissue factor pathway inhibitor (TFPI) polymorphisms are known to be involved in venous thrombosis; however, any correlation between the TFPI polymorphisms rs8176592, rs10931292, and rs10153820 and venous thrombosis remains controversial. This meta-analysis aimed to elucidate the relationship between these TFPI polymorphisms and the susceptibility to venous thrombosis.

METHODS

A literature search for relevant studies was conducted in PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), and Wanfang Med Online databases. Odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs) were calculated using fixed-effect/random-effect models by the STATA 12.0 software. Sources of heterogeneity were analyzed by subgroup analysis.

RESULTS

Eleven case-control studies involving 3740 subjects (1362 venous thrombosis patients and 2378 healthy controls) were included. The TFPI rs8176592 polymorphism was associated with increased risk of venous thrombosis in the whole population, while no significant association was found between rs10931292/rs10153820 and venous thrombosis. In subgroup analysis based on ethnicity, an increased risk was observed with rs8176592 polymorphism in Asians (Recessive model, OR = 1.48, 95% CI = 1.06-2.07, P = .023). An increased risk associated with rs10931292 was identified in non-Asians (Recessive model, OR = 1.42, 95% CI = 1.03-1.97, P = .033). No significant association was found in either Asians or non-Asians with the rs10153820 polymorphism. In subgroup analysis based on source of controls, increased risks were identified in the hospital-based group with rs8176592 polymorphism and in the population-based group with rs10931292 polymorphism, whereas decreased risk was identified in the hospital-based group with the rs10931292 and rs10153820 polymorphisms.

CONCLUSION

Meta-analysis suggested that different TFPI polymorphisms may have different associations with venous thrombosis. TFPI rs8176592 polymorphism may increase the risk of venous thrombosis, especially in Asians and hospital-based patients. The TFPI rs10931292 polymorphism may increase the venous thrombosis risk for both non-Asians and population-based patients. Moreover, rs10931292 and rs10153820 polymorphisms of TFPI may decrease the risk of venous thrombosis for hospital-based patients.

Testing for goodness rather than lack of fit of an X-chromosomal SNP to the Hardy-Weinberg model

The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence testing procedure to be derived by treating approximate compatibility with the model as the alternative hypothesis. The test constructed here is based on an upper confidence bound and a simple to interpret combined measure of distance between true and HWE conforming genotype distributions in female and male subjects. A particular focus of the paper is on the derivation of the asymptotic distribution of the test statistic under null alternatives which is not of the usual Gaussian form. A closed sample size formula is also provided and shown to behave satisfactorily in terms of the approximation error.

Natural killer cells induce neutrophil extracellular trap formation in venous thrombosis

Essentials Neutrophil extracellular traps (NETs) are generated during deep vein thrombosis (DVT). The role of interferon γ (IFNγ) and natural killer (NK) cells in NET formation was studied. IFNγ promote venous thrombosis through NET formation. NK cell depletion reduces DVT. SUMMARY: Background Neutrophils contribute to venous thrombosis through the release of neutrophil extracellular traps (NETs), but the mechanism triggering their formation remains unclear. In vitro data show that interferon (IFN)-γ induces the formation of NETs. Objectives To determine whether IFN-γ and the transcription factor T-box expressed on T cells (Tbet) promote venous thrombosis through neutrophil activation. Methods Venous thrombosis was induced by flow restriction in the inferior vena cava in IFN-γ-/- , Tbet-/- or wild-type (WT) mice. After 48 h, thrombus size was measured by the use of high-frequency ultrasound. NET formation was determined by immunofluorescence. Results and Conclusions Thrombus formation was reduced in Tbet-/- and IFN-γ-/- mice, suggesting that Tbet/IFN-γ-expressing cells are required for venous thrombosis. The number of NETs formed during thrombosis was significantly lower in Tbet-/- and IFN-γ-/- mice. NET formation was also decreased in WT mice treated with an IFN-γ-blocking antibody. Injection of recombinant IFN-γ into IFN-γ-/- mice rescued the phenotype. Natural killer (NK) cells were specifically depleted prior to venous thrombosis induction. NK cell depletion results in decreased NET formation and smaller thrombi, suggesting that NK cells are required for thrombus development. In depleted mice, adoptive transfer of WT NK cells induced a similar thrombosis burden as in WT mice. In contrast, adoptive transfer of IFN-γ -/- NK cells resulted in thrombi similar in size to those in depleted mice. In vitro, we showed that WT neutrophils released fewer NETs when they were cocultured with IFN-γ-/- NK cells. This study demonstrates that NK cell-dependent IFN-γ production is crucial for thrombus development by promoting the formation of NETs by neutrophils.

A novel variation of SERPINC1 caused deep venous thrombosis in a Chinese family: A case report

RATIONALE

Deep vein thrombosis (DVT) is the formation of a blood clot formed in the deep veins of the lower limbs. Known genetic factors of DVT include deficiencies of antithrombin (AT), protein C, protein S, factor V Leiden mutation, and prothrombin G20210A mutation. Here, a 5-generation Chinese family with inherited DVT was recruited for genetic analysis.

PATIENT CONCERNS

The patient came to see a doctor because of leg swelling. A color Doppler ultrasound examination showed extensive thrombosis within the deep veins of her left leg. Computed tomography angiography showed a pulmonary embolism in her right lower pulmonary artery.

DIAGNOSES

Type II AT deficiency lead to inherited DVT.

INTERVENTIONS

Whole-exome sequencing and cosegregation analysis were carried for the DVT family.

OUTCOMES

An unreported heterozygous missense variation, c.281T>C, was identified within the SERPINC1 gene. This missense variation of SERPINC1 leads to type II AT deficiency.

LESSONS

This result further enriched the variation spectrum of the SERPINC1 gene.

Targeted sequencing to identify novel genetic risk factors for deep vein thrombosis: a study of 734 genes

Essentials Deep vein thrombosis (DVT) has a large unknown genetic component. We sequenced coding areas of 734 hemostasis-related genes in 899 DVT patients and 599 controls. Variants in F5, FGA-FGG, CYP4V2-KLKB1-F11, and ABO were associated with DVT risk. Associations in KLKB1 and F5 suggest a more complex genetic architecture than previously thought. SUMMARY: Background Although several genetic risk factors for deep vein thrombosis (DVT) are known, almost all related to hemostasis, a large genetic component remains unexplained. Objectives To identify novel genetic determinants by using targeted DNA sequencing. Patients/Methods We included 899 DVT patients and 599 controls from three case-control studies (DVT-Milan, Multiple Environmental and Genetic Assessment of risk factors for venous thrombosis [MEGA], and the Thrombophilia, Hypercoagulability and Environmental Risks in Venous Thromboembolism [THE-VTE] study) for sequencing of the coding regions of 734 genes involved in hemostasis or related pathways. We performed single-variant association tests for common variants (minor allele frequency [MAF] ≥ 1%) and gene-based tests for rare variants (MAF ≤ 1%), accounting for multiple testing by use of the false discovery rate (FDR). Results Sixty-two of 3617 common variants were associated with DVT risk (FDR < 0.10). Most of these mapped to F5,ABO,FGA-FGG, and CYP4V2-KLKB1-F11. The lead variant at F5 was rs6672595 (odds ratio [OR] 1.58, 95% confidence interval [CI] 1.29-1.92), in moderate linkage with the known variant rs4524. Reciprocal conditional analyses suggested that intronic variation might drive this association. We also observed a secondary association at the F11 region: missense KLKB1 variant rs3733402 remained associated conditional on known variants rs2039614 and rs2289252 (OR 1.36, 95% CI 1.10-1.69). Two novel variant associations were observed, in CBS and MASP1, but these were not replicated in the meta-analysis data from the International Network against Thrombosis (INVENT) consortium. There was no support for a burden of rare variants contributing to DVT risk (FDR > 0.2). Conclusions We confirmed associations between DVT and common variants in F5,ABO,FGA-FGG, and CYP4V2-KLKB1-F11, and observed secondary signals in F5 and CYP4V2-KLKB1-F11 that warrant replication and fine-mapping in larger studies.

Prevalence and geographical variation of Factor V Leiden in patients with cerebral venous thrombosis: A meta-analysis

Background

Previous results regarding the prevalence of Factor V Leiden (FVL) in patients with cerebral venous thrombosis (CVT) varied remarkably. Therefore, we performed a meta-analysis to evaluate the potential association between FVL and CVT.

Methods

The PubMed, Embase, Cochrane Central Register of Controlled Trials, and Web of Science were searched for relevant case-control studies. The data were pooled for analysis of the association between FVL and CVT with a random-effects model. Subgroup and sensitivity analyses were performed to evaluate the robustness of the results. Publication bias was assessed by funnel plot and the Egger’s test.

Results

A total of 39 case-control studies including 1807 cases of CVT and 7699 control cases were included. FVL was more common in patients with CVT (195/1822) than in controls(369/7795), [odds ratio(OR) = 2.70, 95% confidence interval(CI) 2.16–3.38, P < 0.00001]. Results of subgroup analyses indicated that the association between FVL and CVT varied according to geographic regions. The associations between FVL and CVT were significant in studies from Germany (OR = 2.42, 95%CI 1.70–3.45, P < 0.00001), Brazil(OR = 2.82, 95%CI 1.24–6.42, P = 0.01), France (OR = 5.44, 95%CI 1.35–21.92, P = 0.02), Iran (OR = 6.61, 95%CI 1.83–23.93, P = 0.004), and Tunisia (OR = 6.54, 95%CI 2.89–14.82, P < 0.00001), but not in those from Italy (OR = 1.49, 95%CI 0.59–3.78, P = 0.40) or the US (OR = 2.37, 95%CI 0.59–9.42, P = 0.22).

Conclusion

FVL may be more common in patients with CVT. However, the association between FVL and CVT varied depending on the geographic origin of the studies.

Prevalence of CALR mutations in splanchnic vein thrombosis: A systematic review and meta-analysis

BACKGROUND

The prevalence of calreticulin (CALR) mutations in splanchnic vein thrombosis (SVT) varies among studies. The role of routine screening for CALR mutations in SVT patients remains a debate.

AIM

To synthesize the prevalence of CALR mutations according to the different types (i.e., Budd-Chiari syndrome [BCS] and portal vein thrombosis [PVT]) and characteristics (i.e., with and without myeloproliferative neoplasms [MPNs] and JAK2V617F mutation) of SVT patients.

METHODS

Eligible studies were searched by the PubMed and Embase databases. The study quality was assessed according to the STROBE checklist. The proportion of CALR mutations was pooled by using a random-effects model. The heterogeneity and publication bias were calculated.

RESULTS

Eleven papers were included. The study quality was moderate to high. The pooled proportion of CALR mutations was 1.21%, 1.41%, and 1.59% in SVT, BCS, and PVT patients, respectively; 1.52%, 1.03%, and 1.82% in these patients without JAK2V617F mutation, respectively; 3.71%, 2.79%, and 7.87% in these patients with MPN, respectively; and 15.16%, 17.22%, and 31.44% in these patients with MPN but without JAK2V617F mutation, respectively. Only the meta-analysis examining the prevalence of CLAR mutations in BCS patients with MPN but without the JAK2V617F mutation showed statistically significant heterogeneity. Statistically significant publication bias was seen only in the meta-analysis examining the prevalence of CALR mutations in SVT patients without the JAK2V617F mutation.

CONCLUSION

Screening for CALR mutations may have a role in SVT patients with a high probability of MPN in whom the JAK2V617F mutation has been excluded.

Coagulation factor V gene 1691G>A polymorphism as an indicator for risk and prognosis of lower extremity deep venous thrombosis in Chinese Han population

The purpose of this study was to explore the negative influence coagulation factor V (FV) 1691G>A polymorphism had on the risk and prognosis of lower extremity deep venous thrombosis (LDVT) in Chinese Han population.A total of 348 patients with LDVT (LDVT group) and 398 healthy individuals (control group) were selected to further this study. A polymerase chain reaction-restriction fragment length polymorphism method was used to analyze the FV gene 1691G>A polymorphism; coagulation and anticoagulation indexes of patients with LDVT were detected as a result. A 3-year follow-up and logistic regression analysis were conducted to determine the corresponding correlations between FV gene and LDVT.In comparison with the control group, the frequencies of GA and AA genotypes and A allele of 1691G>A polymorphism significantly increased in the LDVT group. Also, in comparison with patients with LDVT carrying GG genotype of FV gene 1691G>A polymorphism, the following activities reduced significantly: prothrombin time, activated partial thromboplastin time, fibrinogen, protein C, and protein S, while activated protein C resistance and lupus anticoagulant positive rate increased in patients carrying A allele (GA + AA). Logistic regression analysis indicated that FV gene 1691G>A polymorphism, total cholesterol, low-density lipoprotein cholesterol, and LDVT family histories were all closely related with LDVT and were subsequent independent risk factors for LDVT. Moreover, patients with LDVT carrying A allele (GA + AA) had both higher patency and recurrence rates than those carrying GG genotype.FV gene 1691G>A polymorphism may be associated with both the risk and prognosis of LDVT, potentially being a useful index for monitoring LDVT prognosis and risk.

Prothrombin: Another Clotting Factor After FV That Is Involved Both in Bleeding and Thrombosis

Clotting factor defects are usually associated with bleeding. About 2 decades ago, 2 polymorphisms, one of FII (G20210A) and another of FV (Arg506Gln), have been shown to be associated with prothrombotic state and venous thrombosis. As a consequence, FII and FV could be considered both as prohemorrhagic factors and prothrombotic conditions. Recently, it has been shown that missense mutations in the prothrombin gene of amino acid Arg596 of exon 14 to Leu596, Gln596, or Trp596 caused the appearance of a thrombophilic state and venous thrombosis. These mutated FII are not associated with bleeding, but only with venous thrombosis. Furthermore, they are all heterozygotes for the mutations. No missense mutation associated with thrombosis has been discovered so far for FV. As a consequence, the prothrombotic activity of FII is the result of a polymorphism and of a missense mutation, whereas that of FV derives only from a polymorphism. The observation that a clotting factor defect may be associated with both bleeding or venous thrombosis depending on the site of the mutation has caused an extensive reevaluation of the blood clotting mechanism.

Anticoagulant Protein S Targets the Factor IXa Heparin-Binding Exosite to Prevent Thrombosis

OBJECTIVE

PS (protein S) is a plasma protein that directly inhibits the coagulation FIXa (factor IXa) in vitro. Because elevated FIXa is associated with increased risk of venous thromboembolism, it is important to establish how PS inhibits FIXa function in vivo. The goal of this study is to confirm direct binding of PS with FIXa in vivo, identify FIXa amino acid residues required for binding PS in vivo, and use an enzymatically active FIXa mutant that is unable to bind PS to measure the significance of PS-FIXa interaction in hemostasis.

APPROACH AND RESULTS

We demonstrate that PS inhibits FIXa in vivo by associating with the FIXa heparin-binding exosite. We used fluorescence tagging, immunohistochemistry, and protein-protein crosslinking to show in vivo interaction between FIXa and PS. Importantly, platelet colocalization required a direct interaction between the 2 proteins. FIXa and PS also coimmunoprecipitated from plasma, substantiating their interaction in a physiological milieu. PS binding to FIXa and PS inhibition of the intrinsic Xase complex required residues K132, K126, and R170 in the FIXa heparin-binding exosite. A double mutant, K132A/R170A, retained full activity but could not bind to PS. Crucially, Hemophilia B mice infused with FIXa K132A/R170A displayed an accelerated rate of fibrin clot formation compared with wild-type FIXa.

CONCLUSIONS

Our findings establish PS as an important in vivo inhibitor of FIXa. Disruption of the interaction between PS and FIXa causes an increased rate of thrombus formation in mice. This newly discovered function of PS implies an unexploited target for antithrombotic therapeutics.