Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors

Identification of multiple novel procoagulant plasma ligands for stabilin-2

BACKGROUND

Damaging STAB2 gene variants are associated with increased venous thromboembolic risk. STAB2 encodes stabilin-2, a clearance receptor, expressed by the liver and spleen. Given its function, it is likely that the prothrombotic state associated with stabilin-2 deficiency is due to reduced procoagulant protein clearance, but the identity of these ligands is unknown.

OBJECTIVES

To identify plasma stabilin-2 ligands using proximity biotinylation proteomics.

METHODS

Cells stably expressing stabilin-2-TurboID were incubated with human plasma and biotin to initiate TurboID labeling of plasma ligands in endocytic vesicles. Biotinylated proteins were purified and identified using mass spectrometry. Candidate plasma ligands with roles in hemostasis were fluorescently labeled and incubated with stabilin-2 expressing and control cells. Flow cytometry assessed ligand surface binding and confocal microcopy assessed colocalization with stabilin-2 and lysosomes. Furthermore, plasma levels of ligands were measured in Stab2-deficient mice and littermate controls.

RESULTS

Twenty-eight stabilin-2 specific ligands were identified. Interactions with von Willebrand factor, fibrinogen, pro(thrombin), heparin cofactor II, high molecular weight kininogen, plasminogen, and C4b-binding protein were probed. Heparin cofactor II, high molecular weight kininogen, plasminogen, and fibrinogen showed binding to stabilin-2 using flow cytometry (>2-fold higher than controls). Confocal microscopy demonstrated stabilin-2 dependent colocalization of all ligands with lysosomes. In Stab2-deficient mice, ligand levels were not significantly increased, suggesting in mice stabilin-2 is not their main clearance receptor.

CONCLUSION

These results confirm the value of proximity labeling proteomics in identifying receptor ligands and suggest damaging STAB2 variants may increase venous thromboembolic risk potentially through altered hemostatic protein clearance.

Congenital Fibrinogen Deficiencies: Not So Rare

Congenital fibrinogen deficiencies (CFDs), traditionally considered rare monogenic disorders, are now recognized as more prevalent and genetically complex than previously thought. Indeed, the symptoms manifested in CFD patients, such as bleeding and thrombosis, are likely to result from variation in several genes rather than solely driven by variants in one of the three fibrinogen genes, FGB, FGA, and FGG. This review highlights recent advances in understanding the genetic causes of CFD and their variability, facilitated by the growing use and availability of next-generation sequencing data. Using gnomAD v4.1.0. data, which includes more than 800,000 individuals, we provide updated global prevalence estimates for CFDs based on frequencies of predicted deleterious variants in FGB, FGA, and FGG. Recessively inherited fibrinogen deficiencies (homozygous genotypes) could be present in around 29 individuals per million, while dominantly inherited deficiencies (heterozygous genotypes) may be present in up to 15,000 per million. These increased estimates can be attributed to the inclusion of broader, more diverse genetic datasets in the new version of gnomAD, thus capturing a greater range of rare variants and homozygous cases.

Regulation of fibrinogen synthesis

The plasma protein fibrinogen is encoded by 3 structural genes (FGA, FGB, and FGG) that are transcribed to mRNA, spliced, and translated to 3 polypeptide chains (Aα, Bβ, and γ, respectively). These chains are targeted for secretion, decorated with post-translational modifications, and assembled into a hexameric "dimer of trimers" (AαBβγ)2. Fully assembled fibrinogen is secreted into the blood as a 340 kDa glycoprotein. Fibrinogen is one of the most prevalent coagulation proteins in blood, and its expression is induced by inflammatory cytokines, wherein circulating fibrinogen levels may increase up to 3-fold during acute inflammatory events. Abnormal levels of circulating fibrinogen are associated with bleeding and thrombotic disorders, as well as several inflammatory diseases. Notably, therapeutic strategies to modulate fibrinogen levels have shown promise in experimental models of disease. Herein, we review pathways mediating fibrinogen synthesis, from gene expression to secretion. Knowledge of these mechanisms may lead to the identification of biomarkers and new therapeutic targets to modulate fibrinogen in health and disease.

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.

A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels

ABSTRACT

Coagulation factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are critical to coagulation and platelet aggregation. We leveraged whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program along with TOPMed-based imputation of genotypes in additional samples to identify genetic associations with circulating FVIII and VWF levels in a single-variant meta-analysis, including up to 45 289 participants. Gene-based aggregate tests were implemented in TOPMed. We identified 3 candidate causal genes and tested their functional effect on FVIII release from human liver endothelial cells (HLECs) and VWF release from human umbilical vein endothelial cells. Mendelian randomization was also performed to provide evidence for causal associations of FVIII and VWF with thrombotic outcomes. We identified associations (P < 5 × 10-9) at 7 new loci for FVIII (ST3GAL4, CLEC4M, B3GNT2, ASGR1, F12, KNG1, and TREM1/NCR2) and 1 for VWF (B3GNT2). VWF, ABO, and STAB2 were associated with FVIII and VWF in gene-based analyses. Multiphenotype analysis of FVIII and VWF identified another 3 new loci, including PDIA3. Silencing of B3GNT2 and the previously reported CD36 gene decreased release of FVIII by HLECs, whereas silencing of B3GNT2, CD36, and PDIA3 decreased release of VWF by HVECs. Mendelian randomization supports causal association of higher FVIII and VWF with increased risk of thrombotic outcomes. Seven new loci were identified for FVIII and 1 for VWF, with evidence supporting causal associations of FVIII and VWF with thrombotic outcomes. B3GNT2, CD36, and PDIA3 modulate the release of FVIII and/or VWF in vitro.

Congenital fibrinogen disorders: Strengthening genotype-phenotype correlations through novel genetic diagnostic tools

Congenital fibrinogen disorders or CFDs are heterogenous, both in clinical manifestation and array of culprit molecular lesions. Correlations between phenotype and genotype remain poorly defined. This review examines the genetic landscape discovered to date for this rare condition. The question of a possible oligogenic model of inheritance influencing phenotypic heterogeneity is raised, with discussion of the benefits and challenges of sequencing technology used to enhance discovery in this space. Considerable work lies ahead in order to achieve diagnostic and prognostic precision and subsequently provide targeted management to this complex cohort of patients.

Whole Genome Analysis of Venous Thromboembolism: the Trans-Omics for Precision Medicine Program

BACKGROUND

Risk for venous thromboembolism has a strong genetic component. Whole genome sequencing from the TOPMed program (Trans-Omics for Precision Medicine) allowed us to look for new associations, particularly rare variants missed by standard genome-wide association studies.

METHODS

The 3793 cases and 7834 controls (11.6% of cases were individuals of African, Hispanic/Latino, or Asian ancestry) were analyzed using a single variant approach and an aggregate gene-based approach using our primary filter (included only loss-of-function and missense variants predicted to be deleterious) and our secondary filter (included all missense variants).

RESULTS

Single variant analyses identified associations at 5 known loci. Aggregate gene-based analyses identified only PROC (odds ratio, 6.2 for carriers of rare variants; P=7.4×10-14) when using our primary filter. Employing our secondary variant filter led to a smaller effect size at PROC (odds ratio, 3.8; P=1.6×10-14), while excluding variants found only in rare isoforms led to a larger one (odds ratio, 7.5). Different filtering strategies improved the signal for 2 other known genes: PROS1 became significant (minimum P=1.8×10-6 with the secondary filter), while SERPINC1 did not (minimum P=4.4×10-5 with minor allele frequency <0.0005). Results were largely the same when restricting the analyses to include only unprovoked cases; however, one novel gene, MS4A1, became significant (P=4.4×10-7 using all missense variants with minor allele frequency <0.0005).

CONCLUSIONS

Here, we have demonstrated the importance of using multiple variant filtering strategies, as we detected additional genes when filtering variants based on their predicted deleteriousness, frequency, and presence on the most expressed isoforms. Our primary analyses did not identify new candidate loci; thus larger follow-up studies are needed to replicate the novel MS4A1 locus and to identify additional rare variation associated with venous thromboembolism.