Genomic and transcriptomic association studies identify 16 novel susceptibility loci for venous thromboembolism

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation data sets, such as Hi-C, have become available across multiple conditions and time points, offering a unique opportunity to examine changes in 3D genome organization and link them to phenotypic changes in normal and disease processes. However, systematic detection of higher-order structural changes across multiple Hi-C data sets remains a major challenge. Existing computational methods either do not model higher-order structural units or cannot model dynamics across more than two conditions of interest. We address these limitations with tree-guided integrated factorization (TGIF), a generalizable multitask nonnegative matrix factorization (NMF) approach that can be applied to time series or hierarchically related biological conditions. TGIF can identify large-scale changes at the compartment or subcompartment levels, as well as local changes at boundaries of topologically associated domains (TADs). Based on benchmarking in simulated and real Hi-C data, TGIF boundaries are more accurate and reproducible across differential levels of noise and sources of technical artifacts, and are more enriched in CTCF. Application to three multisample mammalian data sets shows that TGIF can detect differential regions at compartment, subcompartment, and boundary levels that are associated with significant changes in regulatory signals and gene expression enriched in tissue-specific processes. Finally, we leverage TGIF boundaries to prioritize sequence variants for multiple phenotypes from the NHGRI GWAS catalog. Taken together, TGIF is a flexible tool to examine 3D genome organization dynamics across disease and developmental processes.

The role of germline and somatic mutations in predicting cancer-associated thrombosis: a narrative review

PURPOSE OF REVIEW

Patients with cancer have an increased risk of venous thromboembolism (VTE). Guidelines suggest to use risk assessment tools to guide decisions about thromboprophylaxis, but current tools have modest discriminatory ability. Genetic information from the germline or tumor has the potential to improve VTE prediction. Here, we provide a clinical overview of the current role of genetics in cancer-associated VTE.

RECENT FINDINGS

Germline mutations, such as factor V Leiden and prothrombin G20210A, are associated with a 2- to 2.5-fold increased VTE risk in patients with cancer. Tumor-specific somatic mutations also contribute to VTE risk, such as ALK rearrangements increasing the risk in nonsmall cell lung cancer and IDH1 mutations decreasing the risk in gliomas. Other somatic mutations associated with VTE independent of tumor type include KRAS , STK11 , MET , KEAP1 , CTNNB1 , and CDKN2B . Incorporating data on germline or somatic mutations in risk scores improves discriminatory ability compared with the Khorana score.

SUMMARY

Specific germline and somatic mutations are associated with an increased VTE risk in patients with cancer and potentially improve performance of clinical risk scores. The increasing and widespread use of genetic testing in cancer care provides an opportunity for further development of prediction models incorporating genetic predictors.

Investigating associations between JAK inhibition and venous thromboembolism by systematic mining of large-scale datasets

Janus kinase inhibitors (JAKi) have been associated with an increased risk of venous thromboembolism (VTE) limiting the use of JAKi-based therapy. To improve risk stratification and drug development, it is crucial to understand the implication of dysregulated JAK-Signal Transducers and Activators of Transcription (STAT) signaling in the pathogenesis of VTE. The objective of this study is to clarify the putative genomic vulnerability to dysregulated JAK-STAT signaling in VTE through systematic mining of large-scale datasets generated from studies comparing VTE patients with healthy controls. Particularly, we assess the representation of entities of the JAK-STAT signaling pathway including STAT target genes among sets of miRNA, mRNA, and proteins differentially abundant in VTE patients, and we explore the putative cumulative genetic association of JAK-STAT signaling gene sets to VTE. Genes related to the JAK-STAT pathway were found significantly altered in VTE patients compared to healthy controls, indicating that genes under transcriptional control of STAT may be dysregulated in VTE. In support of this notion, we find a significant overrepresentation of predicted STAT target genes among genes downregulated in VTE patients, and promoter sequences of differentially regulated genes were significantly enriched with STAT transcription factor binding site motifs. Further linking STAT signaling to the molecular signature of VTE, genes targeted by miRNAs differentially regulated in patients are significantly enriched with STAT target genes and genes acting in the JAK-STAT signaling pathway. Together, our findings indicate that disruptions in the JAK-STAT pathway contribute to the molecular profile of VTE. This offers hope for identifying ways to interact with the JAK-STAT pathway that do not carry the risk of VTE.

Molecular signatures associated with venous thromboembolism in children with acute lymphoblastic leukemia

BACKGROUND

Venous thromboembolism (VTE) is a frequent complication of childhood acute lymphoblastic leukemia (ALL).

OBJECTIVES

We aimed to identify molecular markers and signatures of the leukemia microenvironment associated with VTE in childhood ALL by the dual-omics approach of gene expression and DNA methylation profiling.

METHODS

Eligible children aged 1 to 21 years old with newly diagnosed ALL were enrolled in the Dana-Farber Cancer Institute 16-001 trial with available RNA sequencing data from bone marrow at diagnosis. The primary outcome was VTE requiring medical intervention, divided between early events (ETs), within 6 weeks from ALL diagnosis, or late events otherwise. We compared differential gene expression and DNA methylation in children with and without VTE and in the subgroup of children with ETs. The DNA methylation cis-regulation was explored by dual-omics integration. Functional gene set enrichment analyses were performed to assess dysregulated pathways associated with thrombosis. Gene expression profiling-based signature for the thrombosis-free interval was determined using the Kaplan-Meier estimator and log-rank tests.

RESULTS

We included 248 patients (median age, 7.5 years; 78% precursor B-cell ALL), of whom 56 (23%) developed VTE. Genes and metabolic pathways involved in coagulation, platelet activation, and neutrophil extracellular trap formation were associated with ETs. Dual-omics analysis indicated that methylation reprogramming might be responsible for the overexpression of genes involved in neutrophil extracellular trap formation and coagulation in patients with ETs. A prothrombotic gene signature, based on VWF, PF4, and CXCL8 expression, predicted a thrombosis-free interval.

CONCLUSION

This suggests that gene markers and epigenetic regulation of the leukemic microenvironment are drivers of VTE, notably ETs in childhood ALL.

Exploring genetic loci linked to COVID-19 severity and immune response through multi-trait GWAS analyses

Introduction

COVID-19 severity has been linked to immune factors, with excessive immune responses like cytokine storms contributing to mortality. However, the genetic basis of these immune responses is not well understood. This study aimed to explore the genetic connection between COVID-19 severity and blood cell traits, given their close relationship with immunity.

Materials and methods

GWAS summary statistics for COVID-19 and blood cell counts were analyzed using Linkage Disequilibrium Score Regression (LDSC) to estimate genetic correlations and heritabilities. For traits with significant correlations, a Multi-Trait GWAS Analysis (MTAG) was performed to identify pleiotropic loci shared between COVID-19 and blood cell counts.

Results

Our MTAG analysis identified four pleiotropic loci associated with COVID-19 severity, five loci linked to hospitalized cases, and one locus related to general patients. Among these, two novel loci were identified in the high-risk population, with rs55779981 located near RAVER1 and rs73009538 near CARM1. In hospitalized patients, two previously unrecognized loci were detected, namely, rs115545251 near GFI1 and rs3181049 near RAVER1, while in general patients, rs11065822 near CUX2 emerged as a newly identified locus. We also identified potential target genes, including those involved in inflammation signaling (CARM1), endothelial dysfunction (INTS12), and antiviral immune response (RAVER1), which may require further investigation.

Conclusion

Our study offers insights into the genetic overlap between COVID-19 and immune factors, suggesting potential directions for future research and clinical exploration.

Circulating causal protein networks linked to future risk of myocardial infarction

Variations in blood protein levels have been associated with a broad spectrum of complex diseases, including atherosclerotic cardiovascular disease (ACVD). These associations highlight the intricate interplay between local (e.g., cardiovascular) and systemic (non-cardiovascular) factors for the development of ACVD, emphasizing the need for a comprehensive, systems-level understanding of its etiology. To accomplish this, we developed a causal network inference framework by analyzing one of the largest serum proteomics studies to date, the Age, Gene/Environment Susceptibility-Reykjavik Study (AGES), a prospective population-based study of 7,523 serum proteins measured in 5,376 older adults. To reconstruct a causal network of serum proteins, we used cis -acting protein quantitative trait loci (pQTLs) as instrumental variables to infer causal relationships between protein pairs, while accounting for potential unobserved confounding factors. We identified 185 causal protein subnetworks (FDR = 1%, n ≥ 10 members), which collectively interacted with 5,611 target proteins, offering valuable biological insights and an overview of systemic homeostasis. Several subnetworks, many of which interact to establish a hierarchy of directional relationships, were significantly associated with future myocardial infarction and/or its long-term complications like heart failure, as well as with key cardiometabolic traits that contribute to the onset of ACVD.

Fibrinogen genotypes and their impact on recurrence of venous thromboembolism and family history: A prospective population-based study

Venous thromboembolism (VTE) involves blood clot formation in veins, resulting in serious health issues. Fibrinogen, a crucial clotting protein, consists of three polypeptides encoded by the fibrinogen genes: alpha (FGA), beta (FGB) and gamma (FGG). We genotyped most common missense variants in the fibrinogen genes in relation to VTE, recurrence and family history in Malmö Thrombophilia Study, including 1465 VTE patients followed for ~10 years and 429 healthy donors. FGG (rs6063) was significantly associated with increased odds of primary VTE (odds ratio [OR] = 8.2; 95% confidence interval [CI] = 1.05-63.6) after adjusting for age and sex. For recurrent VTE, Cox-regression analysis indicated a higher risk associated with FGA (rs6050) (hazard ratio [HR] = 1.8; 95% CI = 1.1-2.8), with even greater risk for unprovoked recurrent VTE (HR = 2.3; 95% CI = 1.3-4.2), surpassing the well-known factor V Leiden (FVL) (HR = 1.9; 95% CI = 1.2-3.0). Combining risk alleles from FVL and FGA (rs6050) significantly raised the risk for unprovoked recurrent VTE: ≥3 risk alleles (HR = 4.6; 95% CI = 1.9-11.3), two risk alleles (HR = 2.6; 95% CI = 1.4-4.8) and one risk allele (HR = 1.5; 95% CI = 0.8-2.7) compared to 0 risk allele. Prevalence of FGA (rs6050) risk allele was significantly higher in cases with a family history of VTE. We propose FGA (rs6050) as a novel predictor for unprovoked recurrent VTE and it may contribute to the familial occurrence of VTE.

Association between genetic risk and adherence to the Dietary Approaches to Stop Hypertension diet for developing venous thromboembolism

Background

The relationship between diet and venous thromboembolism (VTE) remains unclear, and the joint effects of diet patterns and genetic susceptibility on VTE risk are unknown.

Objectives

Investigate the independent and joint effects of Dietary Approaches to Stop Hypertension (DASH) diet adherence and polygenic risk scores (PRS) on VTE risk.

Methods

A total of 411,539 UK Biobank participants were included. DASH scores were calculated using Food Frequency Questionnaires, and PRS quantified genetic risk. Cox proportional hazard models estimated hazard ratios (HRs) for VTE, assessing interactions between the DASH diet and genetic susceptibility.

Results

During a median follow-up of 13.4 years, 10,543 participants were diagnosed with VTE. Higher DASH scores were associated with a lower VTE risk (HR, 0.87; 95% CI, 0.82-0.92). A low-adherent DASH diet combined with high-genetic risk had the highest VTE risk (HR, 2.78; 95% CI, 2.47-3.14). High DASH scores reduced VTE risk in high-genetic-risk individuals (HR, 0.84; 95% CI, 0.76-0.92). Sex-specific associations were detected in the joint effect and interaction of DASH scores and PRS. Notably, high DASH scores can offset moderate genetic risk among men (HR, 0.79; 95% CI, 0.67-0.94). There were additive interactions between DASH scores and high genetic risk in total subjects and men, while not observed in women.

Conclusion

The DASH diet is associated with reduced VTE risk and can partially offset genetic predisposition. Low adherence to the DASH diet increases VTE risk, particularly in high-genetic-risk individuals. The protective effect of high DASH scores against genetic risks for VTE is more pronounced in males. Precision medicine should consider both diet and genetics for VTE prevention.

The X chromosome's influences on the human brain

Genes on the X chromosome are extensively expressed in the human brain. However, little is known for the X chromosome's impact on the brain anatomy, microstructure, and functional networks. We examined 1045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X chromosome interactions while proposing an atlas outlining dosage compensation for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we found unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.

The risk for psychiatric disorders in offspring from thrombosis-prone pedigrees in Sweden: a nationwide family study

Background

Psychiatric disorders have been associated with venous thromboembolism (VTE). However, to our knowledge, no nationwide study has examined the familial association between VTE and psychiatric disorders.

Objectives

We took a pedigree-based approach and examined the risk of psychiatric disorders in offspring from extended pedigrees according to the densities of VTE in pedigrees.

Methods

This was a Swedish national family study. We identified a total of 482,184 Swedish pedigrees from the Swedish Multigeneration Register containing a mean of 14.2 parents, aunts/uncles, grandparents, and cousins of a core full-sibship that we termed the pedigree offspring (n = 751,060). We then derived 8 empirical classes of these pedigrees based on the density of cases of VTE. The risk was determined in offspring for psychiatric disorders as a function of VTE density in their pedigrees. Diagnoses of VTE and psychiatric disorders (F00-F69) were determined according to the International Classification of Diseases codes in Swedish registers. All results were Bonferroni corrected.

Results

Higher VTE density, especially for females in pedigrees, was significantly but weakly associated in the offspring with a higher risk of psychiatric disorders. Moreover, VTE density in pedigrees was significantly associated in the offspring with substance abuse disorders, mood (affective) disorders, neurotic, stress-related, and somatoform disorders, behavioral syndromes associated with psychological disturbances and physical factors, personality disorders of adult personality and behavior, depression, and anxiety disorders.

Conclusion

Offspring of pedigrees with a high density of VTE, especially for females, are slightly disadvantaged regarding several psychiatric disorders. VTE shares familial susceptibility, albeit weak, with several psychiatric disorders.

Validation of the 5-SNP score for the prediction of venous thromboembolism in a Danish fast-track cohort of 6789 total hip and total knee arthroplasty patients

Background

Venous thromboembolism (VTE) is a serious complication following total hip arthroplasty (THA) and total knee arthroplasty (TKA). Despite improvements with fast-track treatment protocols, 0.5% of patients still develop a VTE within 90-days postoperatively. Previously, the 5-single nucleotide polymorphism (SNP) genetic risk scores (weighted and simplified) were developed to identify people at a high risk for VTE within the general population.

Objectives

We aimed to assess whether the 5-SNP scores could be used to identify high-risk patients in a cohort of fast-track THA/TKA patients.

Methods

A subset of patients from the Lundbeck Centre for Fast-track Hip and Knee Replacement Database was included based on the availability of genetic information. The 5-SNP scores were calculated for these patients, and their discriminatory performance was determined by c-statistic. Furthermore, the 5-SNP scores were added to a simple logistic prediction model containing clinical predictors to assess the added predictive value.

Results

A total of 7753 THA and TKA procedures (6798 patients) were included in this study. The c-statistics for the weighted and simple 5-SNP scores were 0.50 (95% CI, 0.39-0.61) and 0.48 (95% CI, 0.38-0.58), respectively. For the model with clinical predictors, the c-statistic was 0.67 (95% CI, 0.56-0.77). Addition of either of the 5-SNP scores did not improve discrimination in this model.

Conclusion

These findings do not support genetic risk profiling in fast-track THA/TKA patients to predict VTE. Hence, efforts should be directed at optimizing prediction models with clinical predictors.

Predictive value of abnormal expression of MPHOSPH9 in reintervention after high intensity focused ultrasound treatment of uterine fibroids

AIMS

Aberrantly expressed MPHOSPH9 has been reported to be associated with poor prognosis in many diseases. Previous study indicates that MPHOSPH9 is abnormally expressed in patients with uterine fibroids (UFs). This study focused on the possible prognostic value of MPHOSPH9 in UFs patients after high intensity focused ultrasound (HIFU) treatment.

METHODS

A total of 455 UFs patients participated in the study, including 95 patients who needed reintervention (Reintervention group) and 360 patients who did not need reintervention (Non-reintervention group) after HIFU treatment. They volunteered blood samples before HIFU treatment. The relative expression of MPHOSPH9 was assessed by qRT-PCR. Cox regression analysis was performed to assess the prognostic value of MPHOSPH9 and risk factors of postoperative reintervention.

RESULTS

The expression of MPHOSPH9 was markedly elevated in Reintervention, compared to that of the Non-reintervention group (p < 0.001). Five-year follow-up results showed that among these postoperative patients, 95 patients required reintervention and the reintervention time mainly occurred during 10-40 months after surgery. The Cox regression analysis demonstrated that UFs size (hazard ratio = 2.769, 95% confidence interval: 1.366-5.610) and the high MPHOSPH9 expression level (hazard ratio = 3.160, 95% confidence interval: 1.506-6.630) were independent risk factors for postoperative reintervention.

CONCLUSIONS

The enhanced MPHOSPH9 was a potential candidate for predicting postoperative reintervention in UFs patients.

The Prevalence of the Thrombotic SNPs rs6025, rs1799963, rs2066865, rs2289252 and rs8176719 in Patients with Venous Thromboembolism in the Czech Population

IntroductionStudy aimed to determine the occurrence of 5 thrombosis-related single-nucleotide polymorphisms (SNPs) in patients with venous thromboembolism (VTE) (n = 2630) and a control group (n = 2637) in the Czech population.MethodsThe following gene SNPs were detected in both groups: F5 Leiden (rs6025), F2 (rs1799963), FGG, fibrinogen gamma' (rs2066865), F11 (rs2289252) and ABO (rs8176719). Statistical analysis was performed using SAS statistical software with population genetics tools.ResultsHeterozygotes for F5 Leiden were associated with a 5.58-fold and homozygotes F5 Leiden with a 33.46-fold increased risk of VTE. At SNP rs1799963 (F2, prothrombin), only heterozygotes had a significant 3.9-fold increased risk of VTE. The findings at SNP rs2066865 (fibrinogen gamma', FGG) showed a 1.37-fold increased risk of VTE for FGG heterozygotes and a 1.77-fold increased risk of VTE for FGG homozygotes. There is also a significant 1.42-fold increase risk of VTE in the heterozygotes and a 1.80-fold increase risk of VTE in the homozygotes of the SNP rs 2289252 (F11). Further higher increases in the risk of VTE in both variants were found in patients with VTE at rs8176719 (ABO, non-O). It corresponds to a 2.2-fold increase in the risk of VTE in heterozygotes and a 3.5-fold increase in the risk of VTE in homozygotes.ConclusionBesides F5 Leiden and prothrombin mutation, the study suggests that the gene polymorphisms of FGG (rs2066865), F11 (rs2289252) and ABO (rs8176719) play a role as an independent heritable risk factor for VTE in the Czech population.

Biological Aging and Venous Thromboembolism: A Review of Telomeres and Beyond

Although venous thromboembolism (VTE) is the third most common cardiovascular disease, and the risk of VTE increases sharply with advancing age, approximately 40% of VTE cases are currently classified as unprovoked, highlighting the importance of risk factor research. While chronological aging is associated with the risk of VTE, the association with biological aging remains unclear. Biological aging is highly complex, influenced by several dysregulated cellular and biochemical mechanisms. In the last decade, advancements in omics methodologies provided insights into the molecular complexity of biological aging. Techniques such as high-throughput genomics, epigenomics, transcriptomics, proteomics, and metabolomics analyses identified and quantified numerous epigenetic markers, transcripts, proteins, and metabolites. These methods have also revealed the molecular alterations organisms undergo as they age. Despite the progress, there is still a lack of consensus regarding the methods for assessing and validating these biomarkers, and their application lacks standardization. This review gives an overview of biomarkers of biological aging, including telomere length, and their potential role for VTE. Furthermore, we critically examine the advantages and disadvantages of the proposed methods and discuss possible future directions for investigating biological aging in VTE.

[Advances in the genetics of venous thromboembolic disease]

Venous thromboembolism (VTE) is clinically manifested as deep vein thrombosis (DVT) and pulmonary embolism (PE). VTE is the third most prevalent vascular disease after coronary artery and cerebrovascular diseases. VTE is a multifactorial disease caused by the interaction of genetic and acquired risk factors. Genetic heritability is estimated to be 40%-60% based on studies of families, twins, and siblings. The accumulation of information linking genetic variations to VTE risk has rapidly expanded with the continuous advancement of sequencing technology. Currently, mutations in key genes of the coagulation system, anticoagulation system, and fibrinolysis system are constantly being updated, and the functional mechanisms of new genes are receiving gaining attention. This review summarizes the research progress and prospects of key genetic variations associated with venous thromboembolism.

Thrombotic complications post liver transplantation: Etiology and management

Liver transplantation (LT) is the life saving therapeutic option for patients with acute and chronic end stage liver disease. This is a routine procedure with excellent outcomes in terms of patient survival and quality of life post LT. Orthotopic LT (OLT) patients require a critical care as they are prone to variety of post-operative vascular, cardiovascular, biliary, pulmonary and abdominal complications. Thrombotic complications (both arterial and venous) are not uncommon post liver transplant surgery. Such vascular problems lead to increased morbidity and mortality in both donor and graft recipient. Although thromboprophylaxis is recommended in general surgery patients, no such standards exist for liver transplant patients. Drastic advancements of surgical and anesthetic procedures have improvised survival rates of patients post OLT. Despite these, haemostatic imbalance leading to thrombotic events post OLT cause significant graft loss and morbidity and even lead to patient's death. Thus it is extremely important to understand pathophysiology of thrombosis in LT patients and shorten the timing of its diagnosis to avoid morbidity and mortality in both donor and graft recipient. Present review summarizes the current knowledge of vascular complications associated with LT to highlight their impact on short and long-term morbidity and mortality post LT. Also, present report discusses the lacunae existing in the literature regarding the risk factors leading to arterial and venous thrombosis in LT patients.

Sleep patterns, genetic susceptibility, and venous thromboembolism: A prospective study of 384,758 UK Biobank participants

BACKGROUND

Although healthy sleep patterns have been linked to a lower risk of cardiovascular disease in earlier research, it is unclear how beneficial they are for venous thromboembolism (VTE).

AIM

This research aimed to examine the correlation between sleep patterns, genetic susceptibility, and VTE.

METHODS

In the UK Biobank cohort, healthy sleep behaviors were defined as early chronotype, 7-8 hours of sleep each day, no snoring, infrequent insomnia, and infrequent daytime sleepiness. Each of the five criteria was given 1 point, creating a healthy sleep score ranging from 0 to 5. Cox proportional hazards regression models were utilized to examine the associations between genetic susceptibility, healthy sleep score and VTE.

RESULTS

The UK Biobank study included 384,758 participants aged 56.6 ± 8.0 years. After a median of 11.9 years of follow-up, 8,885 (2.3%) participants were diagnosed with VTE. A healthy sleep score inversely affected VTE risk. For participants with a score of 5, the hazard ratio of VTE was 0.813 (95% confidence interval: 0.758-0.873, P<0.001) compared to those with a score ≤2. Early chronotype, sleeping 7-8 hours each day, infrequent insomnia, and infrequent daytime sleepiness were significantly associated with a 7.9%, 8.3%, 5.1%, and 20.7% lower risk of VTE, respectively. In addition, the correlation between sleep pattern and the incidence of VTE was consistent, regardless of genetic susceptibility (P for interaction = 0.366).

CONCLUSIONS

Our secondary analysis of a large-scale prospectively gathered registry revealed that individuals with a healthy sleep pattern are significantly correlated with lower risk of developing VTE, irrespective of genetic susceptibility.

Multi-ancestry polygenic risk scores for venous thromboembolism

Venous thromboembolism (VTE) is a significant contributor to morbidity and mortality, with large disparities in incidence rates between Black and White Americans. Polygenic risk scores (PRSs) limited to variants discovered in genome-wide association studies in European-ancestry samples can identify European-ancestry individuals at high risk of VTE. However, there is limited evidence on whether high-dimensional PRS constructed using more sophisticated methods and more diverse training data can enhance the predictive ability and their utility across diverse populations. We developed PRSs for VTE using summary statistics from the International Network against Venous Thrombosis (INVENT) consortium genome-wide association studies meta-analyses of European- (71 771 cases and 1 059 740 controls) and African-ancestry samples (7482 cases and 129 975 controls). We used LDpred2 and PRS-CSx to construct ancestry-specific and multi-ancestry PRSs and evaluated their performance in an independent European- (6781 cases and 103 016 controls) and African-ancestry sample (1385 cases and 12 569 controls). Multi-ancestry PRSs with weights tuned in European-ancestry samples slightly outperformed ancestry-specific PRSs in European-ancestry test samples (e.g. the area under the receiver operating curve [AUC] was 0.609 for PRS-CSx_combinedEUR and 0.608 for PRS-CSxEUR [P = 0.00029]). Multi-ancestry PRSs with weights tuned in African-ancestry samples also outperformed ancestry-specific PRSs in African-ancestry test samples (PRS-CSxAFR: AUC = 0.58, PRS-CSx_combined AFR: AUC = 0.59), although this difference was not statistically significant (P = 0.34). The highest fifth percentile of the best-performing PRS was associated with 1.9-fold and 1.68-fold increased risk for VTE among European- and African-ancestry subjects, respectively, relative to those in the middle stratum. These findings suggest that the multi-ancestry PRS might be used to improve performance across diverse populations to identify individuals at highest risk for VTE.

Venous thromboembolic disease genetics: from variants to function

Venous thromboembolic disease (VTE) is a prevalent and potentially life-threatening vascular disease, including both deep vein thrombosis and pulmonary embolism. This review will focus on recent insights into the heritable factors that influence an individual's risk for VTE. Here, we will explore not only the discovery of new genetic risk variants but also the importance of functional characterization of these variants. These genome-wide studies should lead to a better understanding of the biological role of genes inside and outside of the canonical coagulation system in thrombus formation and lead to an improved ability to predict an individual's risk of VTE. Further understanding of the molecular mechanisms altered by genetic variation in VTE risk will be accelerated by further human genome sequencing efforts and the use of functional genetic screens.

Genetic landscape of thrombophilia in recurrent miscarriages

The etiology of recurrent miscarriage (RM) is extremely heterogeneous, encompassing genetic, immunological, anatomical, endocrine, thrombophilic, infectious, and uterine abnormalities. Thrombophilia is a major contributor to pregnancy complications, potentially harming the fetus and jeopardizing the continuation of pregnancy. Therefore, successful pregnancy outcomes depend on maintaining a delicate balance between coagulation and fibrinolytic factors, crucial for ensuring the adjustment of the basal plate to facilitate adequate placental perfusion. Despite numerous studies shedding light on the role of thrombophilic factors and genetic variations in RM, the exact pathogenesis remains unclear. It is imperative to systematically rule out thrombophilia and other related factors responsible for pregnancy disorders and RMs to guide appropriate and active management strategies. Addressing thrombophilia continues to present challenges in terms of effective treatment. The current review aims to address the heterogeneity of RM as a therapeutic challenge, emphasizing the need for standardized diagnostic tests and welldesigned multicenter research trials to gather robust, evidence-based data on thrombophilic causes of RM and provide effective treatment. The goal is to enhance the understanding of thrombophilic factors and genetic landscapes associated with RM through various approaches, including candidate gene studies, genome-wide association studies, and high-throughput sequencing. Meta-analyses have underscored the significance of genetic aberrations in RM, highlighting the necessity for identifying critical mutations implicated in the etiopathogenesis of miscarriages to pave the way for implementation of targeted clinical therapies.

Genome-wide investigation of exogenous female hormones, genetic variation, and venous thromboembolism risk

BACKGROUND

Increased risk of venous thromboembolism (VTE) is a life-threatening side effect for users of oral contraceptives (OCs) or hormone therapy (HT).

OBJECTIVES

To investigate the potential for genetic predisposition to VTE in OC or HT users, we conducted a gene-by-environment case-only meta-analysis of genome-wide association studies (GWAS).

METHODS

Use or nonuse of OCs (7 studies) or HT (8 studies) at the time of the VTE event was determined by pharmacy records or self-report. A synergy index (SI) was modeled for each variant in each study and submultiplicative/supramultiplicative gene-by-environment interactions were estimated. The SI parameters were first meta-analyzed across OC and HT studies and subsequently meta-analyzed to obtain an overall estimate. The primary analysis was agnostic GWAS and interrogated all imputed genotypes using a P value threshold of <5.0 × 10-8; secondary analyses were candidate-based.

RESULTS

The VTE case-only OC meta-analysis included 2895 OC users and 6607 nonusers; the case-only HT meta-analysis included 2434 HT users and 12 793 nonusers. In primary GWAS meta-analyses, no variant reached genome-wide significance, but the smallest P value approached statistical significance: rs9386463 (P = 5.03 × 10-8). We tested associations for 138 candidate variants and identified 2 that exceeded statistical significance (0.05/138 = 3.62 × 10-4): F5 rs6025 (P = 1.87 × 10-5; SI, 1.29; previously observed) and F11 rs2036914 (P = 2.0 × 10-4; SI, 0.91; new observation).

CONCLUSION

The candidate variant approach to identify submultiplictive/supramultiplicative associations between genetic variation and OC and HT use identified a new association with common genetic variation in F11, while the agnostic interrogations did not yield new discoveries.

Transcriptome-wide association study and Mendelian randomization in pancreatic cancer identifies susceptibility genes and causal relationships with type 2 diabetes and venous thromboembolism

BACKGROUND

Two important questions regarding the genetics of pancreatic adenocarcinoma (PDAC) are 1. Which germline genetic variants influence the incidence of this cancer; and 2. Whether PDAC causally predisposes to associated non-malignant phenotypes, such as type 2 diabetes (T2D) and venous thromboembolism (VTE).

METHODS

In this study of 8803 patients with PDAC and 67,523 controls, we first performed a large-scale transcriptome-wide association study to investigate the association between genetically determined gene expression in normal pancreas tissue and PDAC risk. Secondly, we used Mendelian Randomization (MR) to analyse the causal relationships among PDAC, T2D (74,124 cases and 824,006 controls) and VTE (30,234 cases and 172,122 controls).

FINDINGS

Sixteen genes showed an association with PDAC risk (FDR <0.10), including six genes not yet reported for PDAC risk (PPIP5K2, TFR2, HNF4G, LRRC10B, PRC1 and FBXL20) and ten previously reported genes (INHBA, SMC2, ABO, PDX1, MTMR6, ACOT2, PGAP3, STARD3, GSDMB, ADAM33). MR provided support for a causal effect of PDAC on T2D using genetic instruments in the HNF4G and PDX1 loci, and unidirectional causality of VTE on PDAC involving the ABO locus (OR 2.12, P < 1e-7). No evidence of a causal effect of PDAC on VTE was found.

INTERPRETATION

These analyses identified candidate susceptibility genes and disease relationships for PDAC that warrant further investigation. HNF4G and PDX1 may induce PDAC-associated diabetes, whereas ABO may induce the causative effect of VTE on PDAC.

FUNDING

National Institutes of Health (USA).

Increased risk of venous thromboembolism in young and middle-aged individuals with hereditary angioedema: a family study

ABSTRACT

Hereditary angioedema (HAE), caused by C1 inhibitor protein deficiency, was recently shown to be associated with an increased risk for venous thromboembolism (VTE). To our knowledge, this is the first national family study of HAE, which aimed to determine the familial risk of VTE. The Swedish Multi-Generation Register was linked to the Swedish National Patient Register for the period of 1964 to 2018. Only patients with HAE with a validated diagnosis were included in the study and were linked to their family members. Hazard ratios (HRs) and 95% confidence intervals (CIs) for VTE were calculated for patients with HAE in comparison with relatives without HAE. Among 2006 individuals (from 276 pedigrees of 365 patients with HAE), 103 individuals were affected by VTE. In total, 35 (9.6%) patients with HAE were affected by VTE, whereas 68 (4.1%) non-HAE relatives were affected (P < .001). The adjusted HR for VTE among patients with HAE was 2.51 (95% CI, 1.67-3.77). Patients with HAE were younger at the first VTE than their non-HAE relatives (mean age, 51 years vs 63 years; P < .001). Before the age of 70 years, the HR for VTE among patients with HAE was 3.62 (95% CI, 2.26-5.80). The HR for VTE for patients with HAE born after 1964 was 8.29 (95% CI, 2.90-23.71). The HR for VTE for patients with HAE who were born in 1964 or earlier was 1.82 (95% CI, 1.14-2.91). HAE is associated with VTE among young and middle-aged individuals in Swedish families with HAE. The effect size of the association is in the order of other thrombophilias. We suggest that HAE may be considered a new rare thrombophilia.

Serum albumin, genetic susceptibility, and risk of venous thromboembolism

Background

Previous research on the association between serum albumin (ALB) and venous thromboembolism (VTE) has produced inconclusive results. The polygenic risk score is constructed from a set of independent risk variants associated with a disorder, enabling the identification of a larger fraction of the population at comparable or greater disease risk. It is still unknown whether ALB and genetic factors jointly contribute to the incidence of VTE.

Objectives

The present study aimed to explore ALB, genetic susceptibility, and the risk of VTE.

Methods

The present investigation was an analysis of prospectively collected data from UK Biobank, a population-based, longitudinal cohort. Cox proportional models were used to calculate hazard ratios and 95% CIs for VTE. The Kaplan-Meier curve was utilized to visualize the cumulative risk of VTE according to different serum ALB levels, and the restricted cubic spline model was leveraged to explore the exposure-response relationship among ALB levels and VTE risk.

Results

During median follow-up of 13.5 years, 11,502 cases with VTE were diagnosed among 417,113 participants in the UK Biobank. The lower ALB levels were associated with a higher risk for VTE. Individuals with both a high genetic risk and lowest ALB level had the highest risk of VTE (hazard ratio, 3.89; 95% CI, 3.41-4.43), compared with those with low genetic risk and highest ALB level. The positive joint effects of low ALB and polygenic risk score increased the risk of VTE in individuals with high genetic risk. This study excluded non-European patients and primarily focused on the European population, which may limit the generalizability of the findings.

Conclusion

Low serum ALB levels were linked to an increased risk of VTE, which was in accordance with a linear dose-response relationship. There was a positive additive effect of ALB and genetic susceptibility on the risk of VTE. ALB could serve as a biomarker for predicting the risk of VTE.

Causal association between circulating blood cell traits and pulmonary embolism: a mendelian randomization study

BACKGROUND

Pulmonary embolism (PE) is a life-threatening thromboembolic disease for which there is limited evidence for effective prevention and treatment. Our goal was to determine whether genetically predicted circulating blood cell traits could influence the incidence of PE.

METHODS

Using single variable Mendelian randomization (SVMR) and multivariate Mendelian randomization (MVMR) analyses, we identified genetic associations between circulating blood cell counts and lymphocyte subsets and PE. GWAS blood cell characterization summary statistics were compiled from the Blood Cell Consortium. The lymphocyte subpopulation counts were extracted from summary GWAS statistics for samples from 3757 individuals that had been analyzed by flow cytometry. GWAS data related to PE were obtained from the FinnGen study.

RESULTS

According to the SVMR and reverse MR, increased levels of circulating white blood cells (odds ratio [OR]: 0.88, 95% confidence interval [CI]: 0.81-0.95, p = 0.0079), lymphocytes (OR: 0.90, 95% CI: 0.84-0.97, p = 0.0115), and neutrophils (OR: 0.88, 95% CI: 0.81-0.96, p = 0.0108) were causally associated with PE susceptibility. MVMR analysis revealed that lower circulating lymphocyte counts (OR: 0.84, 95% CI: 0.75-0.94, p = 0.0139) were an independent predictor of PE. According to further MR results, this association may be primarily related to HLA-DR+ natural killer (NK) cells.

CONCLUSIONS

Among European populations, there is a causal association between genetically predicted low circulating lymphocyte counts, particularly low HLA-DR+ NK cells, and an increased risk of PE. This finding supports observational studies that link peripheral blood cells to PE and provides recommendations for predicting and preventing this condition.

Thrombosis risk in single- and double-heterozygous carriers of factor V Leiden and prothrombin G20210A in FinnGen and the UK Biobank

ABSTRACT

The factor V Leiden (FVL; rs6025) and prothrombin G20210A (PTGM; rs1799963) polymorphisms are 2 of the most well-studied genetic risk factors for venous thromboembolism (VTE). However, double heterozygosity (DH) for FVL and PTGM remains poorly understood, with previous studies showing marked disagreement regarding thrombosis risk conferred by the DH genotype. Using multidimensional data from the UK Biobank (UKB) and FinnGen biorepositories, we evaluated the clinical impact of DH carrier status across 937 939 individuals. We found that 662 participants (0.07%) were DH carriers. After adjustment for age, sex, and ancestry, DH individuals experienced a markedly elevated risk of VTE compared with wild-type individuals (odds ratio [OR] = 5.24; 95% confidence interval [CI], 4.01-6.84; P = 4.8 × 10-34), which approximated the risk conferred by FVL homozygosity. A secondary analysis restricted to UKB participants (N = 445 144) found that effect size estimates for the DH genotype remained largely unchanged (OR = 4.53; 95% CI, 3.42-5.90; P < 1 × 10-16) after adjustment for commonly cited VTE risk factors, such as body mass index, blood type, and markers of inflammation. In contrast, the DH genotype was not associated with a significantly higher risk of any arterial thrombosis phenotype, including stroke, myocardial infarction, and peripheral artery disease. In summary, we leveraged population-scale genomic data sets to conduct, to our knowledge, the largest study to date on the DH genotype and were able to establish far more precise effect size estimates than previously possible. Our findings indicate that the DH genotype may occur as frequently as FVL homozygosity and may confer a similarly increased risk of VTE.

A mouse model of the protease-activated receptor 4 Pro310Leu variant has reduced platelet reactivity

BACKGROUND

Protease-activated receptor 4 (PAR4) mediates thrombin signaling on platelets and other cells. Our recent structural studies demonstrated that a single nucleotide polymorphism in extracellular loop 3 and PAR4-P310L (rs2227376) leads to a hyporeactive receptor.

OBJECTIVES

The goal of this study was to determine how the hyporeactive PAR4 variant in extracellular loop 3 impacts platelet function in vivo using a novel knock-in mouse model (PAR4-322L).

METHODS

A point mutation was introduced into the PAR4 gene F2rl3 via CRISPR/Cas9 to create PAR4-P322L, the mouse homolog to human PAR4-P310L. Platelet response to PAR4 activation peptide (AYPGKF), thrombin, ADP, and convulxin was monitored by αIIbβ3 integrin activation and P-selectin translocation using flow cytometry or platelet aggregation. In vivo responses were determined by the tail bleeding assay and the ferric chloride-induced carotid artery injury model.

RESULTS

PAR4-P/L and PAR4-L/L platelets had a reduced response to AYPGKF and thrombin measured by P-selectin translocation or αIIbβ3 activation. The response to ADP and convulxin was unchanged among genotypes. In addition, both PAR4-P/L and PAR4-L/L platelets showed a reduced response to thrombin in aggregation studies. There was an increase in the tail bleeding time for PAR4-L/L mice. The PAR4-P/L and PAR4-L/L mice both showed an extended time to arterial thrombosis.

CONCLUSION

PAR4-322L significantly reduced platelet responsiveness to AYPGKF and thrombin, which is in agreement with our previous structural and cell signaling studies. In addition, PAR4-322L had prolonged arterial thrombosis time. Our mouse model provides a foundation to further evaluate the role of PAR4 in other pathophysiological contexts.

The pivotal role of the X-chromosome in the genetic architecture of the human brain

Genes on the X-chromosome are extensively expressed in the human brain. However, little is known for the X-chromosome's impact on the brain anatomy, microstructure, and functional network. We examined 1,045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X-chromosome interactions, while proposing an atlas outlining dosage compensation (DC) for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we discovered unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X-chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.

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.

Persistent Peril: Recurrent Deep Vein Thrombosis and Pulmonary Embolism in a Patient With Protein S Deficiency Despite Optimal Anticoagulation Therapies

The clotting system has evolved as an adaptive mechanism to prevent blood loss during vascular damage. However, the intricate nature of the clotting cascade and the complexities of human life can sometimes lead to the unnatural activation of this delicate cascade. This can result in blood clot formation within the cardiovascular system, contributing to a wide range of pathological conditions. Abnormal intravascular coagulation most commonly occurs in the deep veins of the lower extremities, and can emboli to other organs, hence, it is termed "venous thromboembolism" (VTE). In this report, we introduce a challenging case of VTE that poses a dilemma for current medical management. The patient with possible protein S deficiency underwent various guideline-directed medical treatments, yet experienced recurrent VTE episodes, including deep vein thrombosis (DVT) and pulmonary embolism (PE), leading to hospital readmissions. This case report sheds light on our challenges in effectively treating VTE.

Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus

BACKGROUND

Angioedema is a rare but potentially life-threatening adverse drug reaction in patients receiving angiotensin-converting enzyme inhibitors (ACEis). Research suggests that susceptibility to ACEi-induced angioedema (ACEi-AE) involves both genetic and nongenetic risk factors. Genome- and exome-wide studies of ACEi-AE have identified the first genetic risk loci. However, understanding of the underlying pathophysiology remains limited.

OBJECTIVE

We sought to identify further genetic factors of ACEi-AE to eventually gain a deeper understanding of its pathophysiology.

METHODS

By combining data from 8 cohorts, a genome-wide association study meta-analysis was performed in more than 1000 European patients with ACEi-AE. Secondary bioinformatic analyses were conducted to fine-map associated loci, identify relevant genes and pathways, and assess the genetic overlap between ACEi-AE and other traits. Finally, an exploratory cross-ancestry analysis was performed to assess shared genetic factors in European and African-American patients with ACEi-AE.

RESULTS

Three genome-wide significant risk loci were identified. One of these, located on chromosome 20q11.22, has not been implicated previously in ACEi-AE. Integrative secondary analyses highlighted previously reported genes (BDKRB2 [bradykinin receptor B2] and F5 [coagulation factor 5]) as well as biologically plausible novel candidate genes (PROCR [protein C receptor] and EDEM2 [endoplasmic reticulum degradation enhancing alpha-mannosidase like protein 2]). Lead variants at the risk loci were found with similar effect sizes and directions in an African-American cohort.

CONCLUSIONS

The present results contributed to a deeper understanding of the pathophysiology of ACEi-AE by (1) providing further evidence for the involvement of bradykinin signaling and coagulation pathways and (2) suggesting, for the first time, the involvement of the fibrinolysis pathway in this adverse drug reaction. An exploratory cross-ancestry comparison implicated the relevance of the associated risk loci across diverse ancestries.

Genetic associations of protein-coding variants in venous thromboembolism

Previous genetic studies of venous thromboembolism (VTE) have been largely limited to common variants, leaving the genetic determinants relatively incomplete. We performed an exome-wide association study of VTE among 14,723 cases and 334,315 controls. Fourteen known and four novel genes (SRSF6, PHPT1, CGN, and MAP3K2) were identified through protein-coding variants, with broad replication in the FinnGen cohort. Most genes we discovered exhibited the potential to predict future VTE events in longitudinal analysis. Notably, we provide evidence for the additive contribution of rare coding variants to known genome-wide polygenic risk in shaping VTE risk. The identified genes were enriched in pathways affecting coagulation and platelet activation, along with liver-specific expression. The pleiotropic effects of these genes indicated the potential involvement of coagulation factors, blood cell traits, liver function, and immunometabolic processes in VTE pathogenesis. In conclusion, our study unveils the valuable contribution of protein-coding variants in VTE etiology and sheds new light on its risk stratification.

The risk for venous thromboembolism and cardiometabolic disorders in offspring from thrombosis-prone pedigrees

BACKGROUND

Most family studies on venous thromboembolism (VTE) have focused on first-degree relatives.

OBJECTIVES

We took a pedigree-based approach and examined the risk of VTE and cardiometabolic disorders in offspring from extended pedigrees according to the densities of VTE in pedigrees.

METHODS

From the Swedish population, we identified a total of 482 185 pedigrees containing a mean of 14.2 parents, aunts/uncles, grandparents, and cousins of a core full sibship that we termed the pedigree offspring (n = 751 060). We then derived 8 empirical classes of these pedigrees based on the density of cases of VTE. The risk was determined in offspring for VTE and cardiometabolic disorders as a function of VTE density in their pedigrees. Bonferroni correction for multiple comparisons was performed.

RESULTS

VTE was unevenly distributed in the population; the Gini coefficient was 0.59. Higher VTE density in pedigrees was associated in the offspring with a higher risk of different VTE manifestations (deep venous thrombosis, pulmonary embolism, pregnancy-related VTE, unusual thrombosis, and superficial thrombophlebitis), thrombophilia, and lower age of first VTE event. Moreover, VTE density in pedigrees was significantly associated in the offspring with obesity, diabetes, gout, varicose veins, and arterial embolism and thrombosis (excluding brain and heart). No significant associations were observed for retinal vein occlusion, hypercholesterolemia, hypertension, coronary heart disease, myocardial infarction, ischemic stroke, atrial fibrillation, heart failure, primary pulmonary hypertension, cerebral hemorrhage, aortic aneurysm, peripheral artery disease, and overall mortality.

CONCLUSION

Offspring of pedigrees with a high density of VTE are disadvantaged regarding VTE manifestations and certain cardiometabolic disorders.

Research into New Molecular Mechanisms in Thrombotic Diseases Paves the Way for Innovative Therapeutic Approaches

Thrombosis is a multifaceted process involving various molecular components, including the coagulation cascade, platelet activation, platelet-endothelial interaction, anticoagulant signaling pathways, inflammatory mediators, genetic factors and the involvement of various cells such as endothelial cells, platelets and leukocytes. A comprehensive understanding of the molecular signaling pathways and cell interactions that play a role in thrombosis is essential for the development of precise therapeutic strategies for the treatment and prevention of thrombotic diseases. Ongoing research in this field is constantly uncovering new molecular players and pathways that offer opportunities for more precise interventions in the clinical setting. These molecular insights into thrombosis form the basis for the development of targeted therapeutic approaches for the treatment and prevention of thrombotic disease. The aim of this review is to provide an overview of the pathogenesis of thrombosis and to explore new therapeutic options.

Association between venous thromboembolism-associated genetic variants, coagulation factor levels, and thrombin generation potential

Recently three large meta-analyses of genome-wide association studies for venous thromboembolism (VTE) identified over 130 genetic variants. However, mechanisms by which newly identified and therefore underexplored VTE-associated genetic variants influence VTE remain unclear. To elucidate the mechanism, we investigated the association between 61 newly identified VTE-associated genetic variants and the levels of coagulation factor (F) VIII, FIX, FXI, and fibrinogen as well as thrombin generation parameters (lag time, peak, endogenous thrombin potential, time-to-peak, and velocity), which are well-known biological traits associated with VTE. This study was conducted on 5341 participants of the Netherlands Epidemiology of Obesity study. The associations between VTE-associated genetic variants and coagulation factor levels and thrombin generation parameters were examined using linear regression analyses, adjusted for age, sex, body mass index, oral contraceptive use, hormone replacement therapy, and menopausal status. Of 61 genetic variants, 33 were associated with one or more of the coagulation factor levels and thrombin generation parameters. Following multiple testing corrections, five genetic variants remained significant, of which MAP1A rs55707100 exhibited the most robust association with thrombin generation parameters and FXI levels (β = -5.33%, 95% confidence interval: -8.44, -2.22). Our findings shed light on the underlying mechanisms by which these genetic variants influence the risk of VTE.

Proportion of venous thromboembolism attributed to recognized prothrombotic genotypes in men and women

Background

Data on the proportion of venous thromboembolism (VTE) risk attributed to prothrombotic genotypes in men and women are limited.

Objectives

We aimed to estimate the population attributable fraction (PAF) of VTE for recognized, common prothrombotic genotypes in men and women using a population-based case cohort.

Methods

Cases with incident VTE (n = 1493) and a randomly sampled subcohort (n = 13,069) were derived from the Tromsø study (1994-2012) and the Trøndelag Health Study (1995-2008) cohorts. DNA samples were genotyped for 17 single-nucleotide polymorphisms (SNPs) previously associated with VTE. PAFs with 95% bias-corrected CIs (based on 10,000 bootstrap samples) were estimated for SNPs significantly associated with VTE, and a 6-SNP cumulative model was constructed for both sexes.

Results

In women, the individual PAFs for SNPs included in the cumulative model were 16.9% for ABO (rs8176719), 17.6% for F11 (rs2036914), 15.1% for F11 (rs2289252), 8.7% for FVL (rs6025), 6.0% for FGG (rs2066865), and 0.2% for F2 (rs1799963). The cumulative PAF for this 6-SNP model was 37.8%. In men, the individual PAFs for SNPs included in the cumulative model were 21.3% for ABO, 12.2% for F11 (rs2036914), 10.4% for F11 (rs2289252), 7.5% for FVL, 7.8% for FGG, and 1.1% for F2. This resulted in a cumulative PAF in men of 51.9%.

Conclusion

Our findings in a Norwegian population suggest that 52% and 38% of the VTEs can be attributed to known prothrombotic genotypes in men and women, respectively.

Novel Insights in Venous Thromboembolism Risk Assessment Methods in Ambulatory Cancer Patients: From the Guidelines to Clinical Practice

Many cancer patients will experience venous thromboembolism (VTE) at some stage, with the highest rate in the initial period following diagnosis. Novel cancer therapies may further enhance the risk. VTE in a cancer setting is associated with poor prognostic, a decreased quality of life, and high healthcare costs. If thromboprophylaxis in hospitalized cancer patients and perioperative settings is widely accepted in clinical practice and supported by the guidelines, it is not the same situation in ambulatory cancer patient settings. The guidelines do not recommend primary thromboprophylaxis, except in high-risk cases. However, nowadays, risk stratification is still challenging, although many tools have been developed. The Khrorana score remains the most used method, but it has many limits. This narrative review aims to present the current relevant knowledge of VTE risk assessment in ambulatory cancer patients, starting from the guideline recommendations and continuing with the specific risk assessment methods and machine learning models approaches. Biomarkers, genetic, and clinical features were tested alone or in groups. Old and new models used in VTE risk assessment are exposed, underlining their clinical utility. Imaging and biomolecular approaches to VTE screening of outpatients with cancer are also presented, which could help clinical decisions.

Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease

Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD.

Multi-ancestry polygenic risk scores for venous thromboembolism

Venous thromboembolism (VTE) is a significant contributor to morbidity and mortality, with large disparities in incidence rates between Black and White Americans. Polygenic risk scores (PRSs) limited to variants discovered in genome-wide association studies in European-ancestry samples can identify European-ancestry individuals at high risk of VTE. However, there is limited evidence on whether high-dimensional PRS constructed using more sophisticated methods and more diverse training data can enhance the predictive ability and their utility across diverse populations. We developed PRSs for VTE using summary statistics from the International Network against Venous Thrombosis (INVENT) consortium GWAS meta-analyses of European- (71,771 cases and 1,059,740 controls) and African-ancestry samples (7,482 cases and 129,975 controls). We used LDpred2 and PRSCSx to construct ancestry-specific and multi-ancestry PRSs and evaluated their performance in an independent European- (6,261 cases and 88,238 controls) and African-ancestry sample (1,385 cases and 12,569 controls). Multi-ancestry PRSs with weights tuned in European- and African-ancestry samples, respectively, outperformed ancestry-specific PRSs in European- (PRSCSXEUR: AUC=0.61 (0.60, 0.61), PRSCSX_combinedEUR: AUC=0.61 (0.60, 0.62)) and African-ancestry test samples (PRSCSXAFR: AUC=0.58 (0.57, 0.6), PRSCSX_combined AFR: AUC=0.59 (0.57, 0.60)). The highest fifth percentile of the best-performing PRS was associated with 1.9-fold and 1.68-fold increased risk for VTE among European- and African-ancestry subjects, respectively, relative to those in the middle stratum. These findings suggest that the multi-ancestry PRS may be used to identify individuals at highest risk for VTE and provide guidance for the most effective treatment strategy across diverse populations.

Construction and optimization of a polygenic risk model for venous thromboembolism in the Chinese population

BACKGROUND

Venous thromboembolism (VTE) has both environmental and genetic risk factors. It is regulated by polygenes and multisites. The polygenic risk score (PRS) has been widely used because any single genetic biomarker failed to accurately predict the genetic risk of VTE. However, no polygenic risk model has been proposed for VTE in the Chinese population. Thus, we aimed to construct a PRS model for the first episode of VTE in the Chinese population.

METHODS

First, single nucleotide polymorphisms (SNPs) associated with VTE in genome-wide association studies, meta-analyses, and candidate gene studies were screened as variables for the PRS. The logarithm of the odds ratio was used to weight the variables. Second, a training set with simulated data from 1000 cases of VTE and 1000 controls was created with different genotypes and frequencies. Finally, we calculated the area under the receiver operating characteristic curve (AUC) to evaluate the discriminatory ability of the PRS model.

RESULTS

We screened 53 SNPs potentially associated with the first episode of VTE in the Chinese population. The AUC of the PRS-53 model (containing 53 SNPs) was 0.748 (95% confidence interval, 0.727-0.770) in the training set. From the largest weight to the smallest weight, SNPs were incrementally added to the model to calculate the AUC for model optimization. The AUC of the PRS-10 model (containing 10 SNPs) was 0.718 (95% confidence interval, 0.696-0.740), with no statistically significant difference from the AUC for the PRS-53 model.

CONCLUSIONS

The PRS-10 and PRS-53 models showed similar predictive abilities and satisfactory discriminatory power and can be used to predict the genetic risk of the first episode of VTE in the Chinese population. The simplified PRS-10 model is more efficient in clinical practice.

The incidence of the thrombophilic SNPs rs6025, rs1799963, rs2066865, rs2289252, and rs8176719 in chronic thromboembolic pulmonary hypertension

INTRODUCTION

Chronic thromboembolic pulmonary hypertension (CTEPH) and venous thromboembolism (VTE) are thought to share many common risk factors. Our study aimed to determine the frequencies of 5 thrombosis-related gene single nucleotide polymorphisms (SNPs) associated with VTE in patients with CTEPH (n 129) compared with a control group of healthy individuals without a history of VTE (n 2637).

METHODS

The SNPs of the following genes were investigated: F5 (F V Leiden, rs6025), F2 prothrombin (rs1799963), fibrinogen gamma (FGG, rs2066865), F11 (rs2289252) and ABO (non-O, rs8176719) in both groups.

RESULTS

The study found that the rs1799963 variant was more common in patients with chronic thromboembolic pulmonary hypertension (CTEPH) compared to the control group (p < .0001). The GA heterozygous variant showed a significant increase with an odds ratio (OR) of 4.480 (95% CI: 2.344-8.562) or a finding by maximum likelihood analysis (MLA) with p < .0001. Additionally, there was a notable increase in the rs8176719 variant with p < .0001 in CTEPH patients. Both the homozygous G/G variant and the heterozygous -/G variant also showed an increase, with OR of 4.2317 (95% CI: 2.45571-7.2919) and 2.4324 (95% CI: 1.46435-4.0403) respectively, or MLA (p < .0001 and p .0006). The study also revealed a higher prevalence of the heterozygous C/T variant of rs2289252 in CTEPH patients, with an OR of 1.5543 (95% CI: 1.02503-2.3568) or MLA (p .0379).

CONCLUSION

The study suggests that the observed gene polymorphisms F2 (rs1799963), ABO (rs8176719), and F11 (rs2289252) may play a role as independent heritable risk factors in the development of CTEPH.

GENETIC DETERMINANTS OF THROMBOSIS

Venous thromboembolism (VTE) is a major cause of morbidity and mortality in the United States. VTE is caused by genetic and acquired conditions, but the genetic variants that increase the risk of VTE are not fully characterized. Recent genome-wide association studies (GWAS) have discovered novel genetic loci linked to VTE. Some of these loci have been characterized, uncovering new pathways that regulate VTE. Functional characterization of candidate genes discovered by GWAS may reveal new therapeutic targets to treat and prevent abnormal thrombosis or bleeding.

Reassessing the Risk of Venous Thromboembolism (VTE) Events in Women

This research aims to reassess women's risk of venous thromboembolism (VTE) events. We conducted an in-depth analysis of the environmental risk factors associated with VTE and their interactions with gender while also exploring the genetic underpinnings of the disease. VTE is identified as a multifactorial condition influenced by a combination of genetic, non-predisposing, and predisposing environmental factors. We further investigated the genetic basis of VTE, focusing on the identification and analysis of risk loci, as well as gene interaction networks and genetic analyses, which offer significant insights into the pathogenesis of VTE. Recognizing the critical role of gender in assessing VTE risk and developing prevention strategies, this research underscores the necessity of adopting an integrated perspective that accounts for individual vulnerabilities at both genetic and environmental levels to formulate effective preventive measures.

Type 2 Diabetes Modifies the Association of CAD Genomic Risk Variants With Subclinical Atherosclerosis

BACKGROUND

Individuals with type 2 diabetes (T2D) have an increased risk of coronary artery disease (CAD), but questions remain about the underlying pathology. Identifying which CAD loci are modified by T2D in the development of subclinical atherosclerosis (coronary artery calcification [CAC], carotid intima-media thickness, or carotid plaque) may improve our understanding of the mechanisms leading to the increased CAD in T2D.

METHODS

We compared the common and rare variant associations of known CAD loci from the literature on CAC, carotid intima-media thickness, and carotid plaque in up to 29 670 participants, including up to 24 157 normoglycemic controls and 5513 T2D cases leveraging whole-genome sequencing data from the Trans-Omics for Precision Medicine program. We included first-order T2D interaction terms in each model to determine whether CAD loci were modified by T2D. The genetic main and interaction effects were assessed using a joint test to determine whether a CAD variant, or gene-based rare variant set, was associated with the respective subclinical atherosclerosis measures and then further determined whether these loci had a significant interaction test.

RESULTS

Using a Bonferroni-corrected significance threshold of P<1.6×10-4, we identified 3 genes (ATP1B1, ARVCF, and LIPG) associated with CAC and 2 genes (ABCG8 and EIF2B2) associated with carotid intima-media thickness and carotid plaque, respectively, through gene-based rare variant set analysis. Both ATP1B1 and ARVCF also had significantly different associations for CAC in T2D cases versus controls. No significant interaction tests were identified through the candidate single-variant analysis.

CONCLUSIONS

These results highlight T2D as an important modifier of rare variant associations in CAD loci with CAC.

Genomic science of risk prediction for venous thromboembolic disease: convenient clarification or compounding complexity

Venous thromboembolism (VTE) refers to abnormal blood clots in veins occurring in 1 to 2 per 1000 individuals every year. While anticoagulant treatment can prevent VTE, it increases the risk of bleeding. This emphasizes the importance of identifying individuals with a high risk of VTE and providing prophylactic interventions to these individuals to reduce both VTE and bleeding risks. Current risk assessment of VTE is based on the combination of mainly clinical risk factors. With the identification of an increasing number of genetic variants associated with the risk of VTE, the addition of genetic findings to clinical prediction models can improve risk prediction for VTE. Especially for individuals in high-risk situations, the added value of genetic findings to clinical prediction models may have benefits such as better prophylaxis of VTE and the reduced side effects of bleeding from unnecessary treatment. Nevertheless, the question of whether these models will eventually have clinical utility remains to be proven. Here, we review the current state of knowledge on genetic risk factors for VTE, explore genetic prediction models for VTE, and discuss their clinical implications and challenges.

A Mouse Model of the Protease Activated Receptor 4 (PAR4) Pro310Leu Variant has Reduced Platelet Reactivity

Background

Protease activated receptor 4 (PAR4) mediates thrombin signaling on platelets and other cells. Our recent structural studies demonstrated a single nucleotide polymorphism in extracellular loop 3 (ECL3), PAR4-P310L (rs2227376) leads to a hypo-reactive receptor.

Objectives

The goal of this study was to determine how the hypo-reactive PAR4 variant in ECL3 impacts platelet function in vivo using a novel knock-in mouse model (PAR4-322L).

Methods

A point mutation was introduced into the PAR4 gene, F2rl3, via CRISPR/Cas9 to create PAR4-P322L, the mouse homolog to human PAR4-P310L. Platelet response to PAR4 activation peptide (AYPGKF), thrombin, ADP, and convulxin was monitored by αIIbβ3 integrin activation and P-selectin translocation using flow cytometry or platelet aggregation. In vivo responses were determined by the tail bleeding assay and the ferric chloride-induced carotid artery injury model.

Results

PAR4-P/L and PAR4-L/L platelets had a reduced response to AYPGKF and thrombin measured by P-selectin translocation or αIIbβ3 activation. The response to ADP and convulxin was unchanged among genotypes. In addition, both PAR4-P/L and PAR4-L/L platelets showed a reduced response to thrombin in aggregation studies. There was an increase in the tail bleeding time for PAR4-L/L mice. The PAR4-P/L and PAR4-L/L mice both showed an extended time to arterial thrombosis.

Conclusions

PAR4-322L significantly reduced platelet responsiveness to AYPGKF and thrombin, which is in agreement with our previous structural and cell signaling studies. In addition, PAR4-322L had prolonged arterial thrombosis time. Our mouse model provides a foundation to further evaluate the role of PAR4 in other pathophysiological contexts.

Proteome-wide mendelian randomization identifies causal plasma proteins in venous thromboembolism development

Genome-wide association studies (GWAS) have identified numerous risk loci for venous thromboembolism (VTE), but it is challenging to decipher the underlying mechanisms. We employed an integrative analytical pipeline to transform genetic associations to identify novel plasma proteins for VTE. Proteome-wide association studies (PWAS) were determined by functional summary-based imputation leveraging data from a genome-wide association analysis (14,429 VTE patients, 267,037 controls), blood proteomes (1348 cases), followed by Mendelian randomization, Bayesian colocalization, protein-protein interaction, and pathway enrichment analysis. Twenty genetically regulated circulating protein abundances (F2, F11, ABO, PLCG2, LRP4, PLEK, KLKB1, PROC, KNG1, THBS2, SERPINA1, RARRES2, CEL, GP6, SERPINE2, SERPINA10, OBP2B, EFEMP1, F5, and MSR1) were associated with VTE. Of these 13 proteins demonstrated Mendelian randomized correlations. Six proteins (F2, F11, PLEK, SERPINA1, RARRES2, and SERPINE2) had strong support in colocalization analysis. Utilizing multidimensional data, this study suggests PLEK, SERPINA1, and SERPINE2 as compelling proteins that may provide key hints for future research and possible diagnostic and therapeutic targets for VTE.

A signature of platelet reactivity in CBC scattergrams reveals genetic predictors of thrombotic disease risk

Genetic studies of platelet reactivity (PR) phenotypes may identify novel antiplatelet drug targets. However, such studies have been limited by small sample sizes (n < 5000) because of the complexity of measuring PR. We trained a model to predict PR from complete blood count (CBC) scattergrams. A genome-wide association study of this phenotype in 29 806 blood donors identified 21 distinct associations implicating 20 genes, of which 6 have been identified previously. The effect size estimates were significantly correlated with estimates from a study of flow cytometry-measured PR and a study of a phenotype of in vitro thrombus formation. A genetic score of PR built from the 21 variants was associated with the incidence rates of myocardial infarction and pulmonary embolism. Mendelian randomization analyses showed that PR was causally associated with the risks of coronary artery disease, stroke, and venous thromboembolism. Our approach provides a blueprint for using phenotype imputation to study the determinants of hard-to-measure but biologically important hematological traits.

Polygenic risk scores for prediction of cancer-associated venous thromboembolism in the UK Biobank cohort study

BACKGROUND

Guidelines recommend thromboprophylaxis for patients with cancer at high risk of venous thromboembolism (VTE). Polygenic risk scores may improve VTE prediction but have not yet been evaluated in patients with cancer.

OBJECTIVES

We assessed the performance of the 5-, 37-, 297-, extended 297- (additionally including factor V Leiden and prothrombin G20210A), and 100-single-nucleotide polymorphism (SNP) scores in predicting cancer-associated VTE in the UK Biobank, a population-based, prospective cohort study.

METHODS

The primary outcome was VTE during 12 months after cancer diagnosis. Cancer and VTE diagnosis were based on ICD-10 codes. Discrimination was evaluated by c-indices and subdistribution hazard ratios in the upper vs 3 lower quartiles of the scores in a competing risk model. As a comparison, the c-index was calculated for the Khorana cancer type risk classification.

RESULTS

Of 36 150 patients with cancer (median age, 66 years; 48.7% females), 1018 (2.8%) developed VTE. C-indices at 12 months ranged from 0.56 (95% CI, 0.54-0.58) for the 5-SNP to 0.60 (95% CI, 0.58-0.62) for the extended 297-SNP scores. The subdistribution hazard ratios ranged from 1.36 (95% CI, 1.19-1.56) for the 5-SNP to 1.90 (95% CI, 1.68-2.16) for the extended 297-SNP scores and were consistent after adjusting for cancer type. For the Khorana cancer type classification, the c-index was 0.60 (95% CI, 0.58-0.61), which increased to 0.65 (95% CI, 0.63-0.67, +0.05; 95% CI, 0.04-0.07) when combined with the extended 297-SNP score.

CONCLUSION

These findings demonstrate that polygenic VTE risk scores can identify patients with cancer with a 1.9-fold higher VTE risk independent of cancer type. Combined clinical-genetic scores to improve cancer-associated VTE prediction should be evaluated further.

Impact of Genetic Variations on Thromboembolic Risk in Saudis with Sickle Cell Disease

BACKGROUND

Sickle cell disease (SCD) is a Mendelian disease characterized by multigenic phenotypes. Previous reports indicated a higher rate of thromboembolic events (TEEs) in SCD patients. A number of candidate polymorphisms in certain genes (e.g., FVL, PRT, and MTHFR) were previously reported as risk factors for TEEs in different clinical conditions. This study aimed to genotype these genes and other loci predicted to underlie TEEs in SCD patients.

METHODOLOGY

A multi-center genome-wide association study (GWAS) involving Saudi SCD adult patients with a history of TEEs (n = 65) and control patients without TEE history (n = 285) was performed. Genotyping used the 10× Affymetrix Axiom array, which includes 683,030 markers. Fisher's exact test was used to generate p-values of TEE associations with each single-nucleotide polymorphism (SNP). The haplotype analysis software tool version 1.05, designed by the University of Göttingen, Germany, was used to identify the common inherited haplotypes.

RESULTS

No association was identified between the targeted single-nucleotide polymorphism rs1801133 in MTHFR and TEEs in SCD (p = 0.79). The allele frequency of rs6025 in FVL and rs1799963 in PRT in our cohort was extremely low (<0.01); thus, both variants were excluded from the analysis as no meaningful comparison was possible. In contrast, the GWAS analysis showed novel genome-wide associations (p < 5 × 10-8) with seven signals; five of them were located on Chr 11 (rs35390334, rs331532, rs317777, rs147062602, and rs372091), one SNP on Chr 20 (rs139341092), and another on Chr 9 (rs76076035). The other 34 SNPs located on known genes were also detected at a signal threshold of p < 5 × 10-6. Seven of the identified variants are located in olfactory receptor family 51 genes (OR51B5, OR51V1, OR51A1P, and OR51E2), and five variants were related to family 52 genes (OR52A5, OR52K1, OR52K2, and OR52T1P). The previously reported association between rs5006884-A in OR51B5 and fetal hemoglobin (HbF) levels was confirmed in our study, which showed significantly lower levels of HbF (p = 0.002) and less allele frequency (p = 0.003) in the TEE cases than in the controls. The assessment of the haplotype inheritance pattern involved the top ten significant markers with no LD (rs353988334, rs317777, rs14788626882, rs49188823, rs139349992, rs76076035, rs73395847, rs1368823, rs8888834548, and rs1455957). A haplotype analysis revealed significant associations between two haplotypes (a risk, TT-AA-del-AA-ins-CT-TT-CC-CC-AA, and a reverse protective, CC-GG-ins-GG-del-TT-CC-TT-GG-GG) and TEEs in SCD (p = 0.024, OR = 6.16, CI = 1.34-28.24, and p = 0.019, OR = 0.33, CI = 0.13-0.85, respectively).

CONCLUSIONS

Seven markers showed novel genome-wide associations; two of them were exonic variants (rs317777 in OLFM5P and rs147062602 in OR51B5), and less significant associations (p < 5 × 10-6) were identified for 34 other variants in known genes with TEEs in SCD. Moreover, two 10-SNP common haplotypes were determined with contradictory effects. Further replication of these findings is needed.