Genetic determinants of normal variation in coagulation factor (F) IX levels: genome-wide scan and examination of the FIX structural gene

Complete F9 Gene Deletion, Duplication, and Triplication Rearrangements: Implications for Factor IX Expression and Clinical Phenotypes

BACKGROUND

 Factor IX (FIX) plays a critical role in blood coagulation. Complete deletion of F9 results in severe hemophilia B, whereas the clinical implications of complete F9 duplication and triplication remain understudied.

OBJECTIVE

 To investigate the rearrangement mechanisms underlying complete F9 deletion (cases 1 and 2), duplication (cases 3 and 4), and triplication (case 5), and to explore their association with FIX expression levels and clinical impacts.

METHODS

 Plasma FIX levels were detected using antigen and activity assays. CNVplex technology, optical genome mapping, and long-distance polymerase chain reaction were employed to characterize the breakpoints of the chromosomal rearrangements.

RESULTS

 Cases 1 and 2 exhibited FIX activities below 1%. Case 3 displayed FIX activities within the reference range. However, cases 4 and 5 showed a significant increase in FIX activities. Alu-mediated nonallelic homologous recombination was identified as the cause of F9 deletion in case 1; FoSTeS/MMBIR (Fork Stalling and Template Switching/microhomology-mediated break-induced replication) contributed to both F9 deletion and tandem duplication observed in cases 2 and 3; BIR/MMBIR (break-induced replication/microhomology-mediated break-induced replication) mediated by the same pair of low-copy repeats results in similar duplication-triplication/inversion-duplication (DUP-TRP/INV-DUP) rearrangements in cases 4 and 5, leading to complete F9 duplication and triplication, respectively.

CONCLUSION

 Large deletions involving the F9 gene exhibit no apparent pattern, and the extra-hematologic clinical phenotypes require careful analysis of other genes within the deletion. The impact of complete F9 duplication and triplication on FIX expression might depend on the integrity of the F9 upstream sequence and the specific rearrangement mechanisms. Notably, DUP-TRP/INV-DUP rearrangements significantly elevate FIX activity and are closely associated with thrombotic phenotypes.

Padua FIXa resistance to Protein S and a potential therapy for hyperactive FIXa

INTRODUCTION

Abnormalities in the levels and functions of proteins that maintain hemostasis can cause thrombosis. Factor IX (FIX) R338L, i.e., Factor IX Padua, is a hyperactive clotting factor that promotes thrombosis. The R338L mutation increases the clotting rate by 8-fold despite increasing the Factor IXa enzymatic activity by only 2-fold. Protein S (PS) is a natural anticoagulant that directly inhibits FIXa. Because individuals affected by the R338L mutation have normal concentrations of PS, we speculated that the Padua hypercoagulation phenotype is due to decreased inhibition of FIXa R338L by PS.

METHODS

We measured the ability of PS to inhibit FIX R338L, and we assessed the ability of PS to mitigate the prothrombotic effect FIX R338L.

RESULTS

Plasma clotting assays demonstrated that 3-fold more PS was required to inhibit FIXa R338L compared with inhibition of wild type FIXa. Thrombin generation assays with Padua patient plasma recapitulated this biochemical consequence of the R338L mutation. Importantly, the less efficient inhibition of FIXa R338L was reversed by increasing PS concentration. Binding and co-immunoprecipitation studies revealed that the decrease in the inhibition of FIXa R338L by PS was caused by a 3- to 4-fold reduction in FIXa R338L affinity for PS.

CONCLUSION

In summary, the resistance of FIXa R338L to inhibition by PS likely contributes to the unexpectedly high clotting rate in Padua individuals. Moreover, PS-mediated reversal of the pathological properties of FIXa R338L suggests that PS administration may be a novel and effective means to mitigate thrombophilia caused by any source of elevated FIXa activity.

The Central Role of KNG1 Gene as a Genetic Determinant of Coagulation Pathway-Related Traits: Exploring Metaphenotypes

Traditional genetic studies of single traits may be unable to detect the pleiotropic effects involved in complex diseases. To detect the correlation that exists between several phenotypes involved in the same biological process, we introduce an original methodology to analyze sets of correlated phenotypes involved in the coagulation cascade in genome-wide association studies. The methodology consists of a two-stage process. First, we define new phenotypic meta-variables (linear combinations of the original phenotypes), named metaphenotypes, by applying Independent Component Analysis for the multivariate analysis of correlated phenotypes (i.e. the levels of coagulation pathway–related proteins). The resulting metaphenotypes integrate the information regarding the underlying biological process (i.e. thrombus/clot formation). Secondly, we take advantage of a family based Genome Wide Association Study to identify genetic elements influencing these metaphenotypes and consequently thrombosis risk. Our study utilized data from the GAIT Project (Genetic Analysis of Idiopathic Thrombophilia). We obtained 15 metaphenotypes, which showed significant heritabilities, ranging from 0.2 to 0.7. These results indicate the importance of genetic factors in the variability of these traits. We found 4 metaphenotypes that showed significant associations with SNPs. The most relevant were those mapped in a region near the HRG, FETUB and KNG1 genes. Our results are provocative since they show that the KNG1 locus plays a central role as a genetic determinant of the entire coagulation pathway and thrombus/clot formation. Integrating data from multiple correlated measurements through metaphenotypes is a promising approach to elucidate the hidden genetic mechanisms underlying complex diseases.

An unusual case of pleural-based tumor with life-threatening post-operative complication

A 57-year-old male presented with hemoptysis of 4 years duration and a gradually increasing pleural mass on chest X-ray. The mass was causing pressure effects on the liver and the lungs. To rule out malignancy, thoracotomy was performed, which revealed large, thick-walled hematoma. Complete excision of mass was performed. Post-operative course was complicated by massive pleural bleeding requiring massive blood transfusions and re-exploratory thoracotomy. Subsequent tests revealed factor IX deficiency and, hence, he was managed with recombinant factor IX concentrate. This case stresses upon the fact that hereditary bleeding disorders may be diagnosed even in late adulthood with atypical presentations such as pseudotumor in pleural space. Moreover, hemophilia B may present with normal APTT levels making the diagnosis even more difficult.

Factor IXa as a target for pharmacologic inhibition in acute coronary syndrome

Anticoagulant therapy, combined with platelet-directed inhibitors, represents a standard-of-care in the management of patients with acute coronary syndrome, particularly those who require percutaneous coronary interventions. While a vast clinical experience, coupled with large clinical trials have collectively provided guidance, an optimal anticoagulant drug and applied strategy, defined as one that reduces thrombotic and hemorrhagic events consistently, with minimal off-target effects and active control of systemic anticoagulation according to patient and clinical-setting specific need, remains at large. An advancing knowledge of coagulation, hemostasis, and thrombosis suggests that factor IXa, a protease that governs thrombin generation in common thrombotic disorders may represent a prime target for pharmacologic inhibition.

Influence of the F12 -4 C>T polymorphism on hemostatic tests

The common F12 -4 C>T polymorphism significantly regulates plasma levels of FXII, the first element of the intrinsic pathway of coagulation. Due to the robust effects that this pathway has on blood coagulation in vitro, the objective of our study was to evaluate the influence of this polymorphism on different hemostatic tests. We studied 46 hemostatic parameters in 566 participants: 280 patients with mucocutaneous bleeding and 286 controls. The F12 -4T allele, associated with reduced levels of FXII (P < 0.001), also significantly delayed the activated partial thromboplastin time (aPTT) expressed as aPTTr (ratio sample plasma/normal pooled plasma). Thus, both patients and controls carrying the T allele had higher aPTTr than C/C homozygous individuals (P < 0.001). Interestingly, 92% of healthy controls who had prolonged aPTTr carried the F12 -4T allele. Moreover, individuals with the F12 -4T allele also had less thrombin generation (assessed by endogenous thrombin potential, thrombin peak and time to achieve the peak of thrombin) using a test with low tissue factor concentration and explicit contact phase activation. Finally, both patients and controls carrying the F12 -4T allele also displayed significantly lower FIXc and FVIIc levels than C/C individuals (P < 0.01). For all associations except for FVIIc, a gene-dosage effect was observed, and homozygous TT individuals had the farthest values. Our study reveals a significant effect of the F12 -4 C>T polymorphism on hemostatic tests widely used in routine clinical practice.

Deciphering the molecular basis of venous thromboembolism: where are we and where should we go?

Venous thromboembolism (VTE) is a frequent disease that has a major genetic component of risk. However, known identified genetic risk factors account for <30% of idiopathic (without any environmental origin) VTE cases. This article aims to review the lessons learnt during recent decades in the field of the genetics of VTE, describe the present state-of-art methods and discuss promising themes for finding new susceptibility loci.

X-linked thrombophilia with a mutant factor IX (factor IX Padua)

We report a case of juvenile thrombophilia associated with a substitution of leucine for arginine at position 338 (R338L) in the factor IX gene (factor IX-R338L). The level of the mutant factor IX protein in plasma was normal, but the clotting activity of factor IX from the proband was approximately eight times the normal level. In vitro, recombinant factor IX-R338L had a specific activity that was 5 to 10 times as high as that in the recombinant wild-type factor IX. The R338 substitution causes a gain-of-function mutation, resulting in factor IX that is hyperfunctional.

Hemophilia B is a quasi-quantitative condition with certain mutations showing phenotypic plasticity

Hemophilia B has been considered as a classical monogenic disorder with complete penetrance. Here, we observed that its allelic spectrum encompasses mutations that show least phenotypic variation as well as those showing phenotypic plasticity, thereby establishing hemophilia B as a quasi-quantitative condition with variable expressivity. Thus, we relocate it from simple monogenic diseases with complete penetrance into a space that marks the conceptual continuum of Mendelian to complex diseases. By computational analysis, we show that mutations showing phenotypic variation were characterized by relatively less conserved mutant sites and more tolerated conservative substitutions. We also demonstrate that consideration of continuous phenotypes renders quantitative rigor for interrogation and hence higher predictive value while analyzing for differential properties than classifications based on clinical end points. Certain mutations have been consistently reported to cause mild phenotype, calling for a check in indiscriminate termination of fetuses following prenatal diagnosis.

F9 Malmö, factor IX and deep vein thrombosis

BACKGROUND

We recently reported the association between the Malmö sequence variant in F9 (rs6048) and deep vein thrombosis.

DESIGN AND METHODS

We aimed to study whether the association between F9 Malmö and deep vein thrombosis is explained by linkage disequilibrium with nearby single-nucleotide polymorphisms, and whether the association is explained biologically by F9 Malmö affecting factor IX antigen levels or activation of factor IX. We investigated the association of F9 Malmö and 28 nearby single-nucleotide polymorphisms with deep vein thrombosis in men from two case-control studies, LETS (n=380) and MEGA (n=1,469). We assessed the association of F9 Malmö with factor IX antigen level in male control subjects from LETS (n=191) and two subsets of MEGA (n=823 and n=484) and the association with endogenous thrombin potential in LETS control men. We studied the association between F9 Malmö and factor IX activation peptide in 1,199 healthy middle-aged men from the NPHS-II cohort.

RESULTS

In the combined LETS and MEGA studies, the odds ratio (95% confidence interval) for the G allele of F9 Malmö, compared with the A allele, was 0.80 (0.69-0.93). One single-nucleotide polymorphism in F9, rs422187, was strongly linked to F9 Malmö (r(2)=0.94) and was similarly associated with deep vein thrombosis. No other single-nucleotide polymorphism or haplotype tested was more strongly associated. Factor IX antigen level, factor IX activation peptide levels and endogenous thrombin potential did not differ between F9 Malmö genotypes.

CONCLUSIONS

The F9 Malmö sequence variant was the most strongly associated with deep vein thrombosis among common single-nucleotide polymorphisms in the region. However, the biological mechanism by which F9 Malmö affects risk remains unknown.

Variability in bleeding phenotype in Amish carriers of haemophilia B with the 31008 C-->T mutation

The aim of this study was to characterize the variability of bleeding phenotype and its association with plasma factor IX coagulant activity (FIX:C) in haemophilia B carriers in a large Amish pedigree with a unifying genetic mutation, C-to-T transition at base 31008 of the factor IX gene (Xq27.1-27.2). A cross-sectional survey of haemophilia B carriers included a multiple choice questionnaire evaluating symptoms of mucocutaneous bleeding, joint bleeding and bleeding after haemostatic stress [menstruation, postpartum haemorrhage (PPH), dental extractions and invasive surgeries]. Severity of bleeding was graded as 0 to 4, 0 being no bleeding whereas 4 being severe bleeding. Association between total bleeding scores and the FIX:C was evaluated. Sixty-four haemophilia B carriers participated in this study. Median age: 18 years (range 1-70 years); median bleeding score: 1 (range 0-8). Besides PPH, isolated symptoms of bruising, epistaxis, menorrhagia and postsurgical bleeding including dental extraction were not associated with lower FIX:C. Bleeding score >/=3 was associated with involvement of at least two bleeding sites and a lower mean FIX:C of 42 +/- 10.3% (95% CI 36.4-47.7) while a score >3 had involvement of </=2 sites and higher mean FIX:C of 54.9 +/- 21.5% (95% CI 49-61), P = 0.005. Subcutaneous haematoma formation and bleeding after haemostatic stress requiring treatment were associated with bleeding scores >/=3. Phenotypic variability existed among the carriers of haemophilia B who belonged to a single pedigree carrying a single unifying mutation. The utility of bleeding scores to define bleeding phenotype precisely in haemophilia B carriers needs further evaluation.

Past and future of genetic research in thrombosis

Genetic studies in thrombosis started with coining of the term thrombophilia by Jordan and Nandorff in 1956. Next, antithrombin deficiency was identified in 1965 as a simple genetic entity that increased thrombotic risk, albeit in a small subset of patients. This subset was enlarged when, in the 1980s, family studies showed that deficiency of protein C (PC) or its co-factor protein S (PS) increased thrombotic risk. Ten years later activated PC resistance and the underlying genetic trait of factor V Leiden were discovered in a family setting. This genetic risk factor was the first prothrombotic defect in a procoagulant protein and was also more prevalent than abnormalities in anticoagulant proteins. The high incidence induced a shift from family studies to case-control studies. Case-control studies became even more popular after the common prothrombin 20,210 mutation was discovered in 1996. In fact, in the last decade common genetic variations in almost all coagulation proteins were tested in association studies. These common variants impart a small risk, if any risk at all, thereby limiting their usefulness in furthering insight into the pathophysiology of thrombosis. Moreover, common risk factors for venous thrombosis fail to improve prediction models for thrombosis on which prophylactic treatment can be tailored. Now that large-scale sequencing techniques are becoming available that enable many genes to be studied in a single individual, one can expect a revival of the identification of private mutations that are associated with large risks, in particular in genes that have been only poorly studied.

Plasma coagulation factor levels in venous thrombosis

High plasma levels of several coagulation factors have been described to be associated with an increased risk of venous thrombosis. However, the mechanisms underlying these associations, as well as those involved in the regulation of plasma levels of coagulation factors, are mostly unknown. Whether these factors should be included in the workup of patients with venous thrombosis remains to be determined. In this review, we discuss the present knowledge on the effects of plasma levels of coagulation factors on the development of venous thrombosis. Furthermore, we review recent findings and ideas on the mechanisms through which elevated plasma coagulation factor levels may influence thrombosis. Finally, we enter into the matter of the possible determinants of elevated plasma levels of coagulation factors.