Biology subjects

Yaman, M.

Publications and source records attributed to Yaman, M..

5 recordsLinked to original sources

bioRxiv2026

A sensitized model of thrombosis validates known multigenic relationships and suggests novel modifiers of hemostasis

BackgroundVenous thromboembolism is a major cause of morbidity and mortality. Despite identification of risk factors, not all individuals with thrombophilia develop thrombosis. Understanding the multigenic factors modifying this incomplete penetrance would help guide patient care. MethodsThe zebrafish has a conserved hemostatic system and is amenable to large genetic studies. Loss of antithrombin III (At3) in zebrafish leads to an early consumptive coagulopathy and lethality in adulthood. Using this genetic background as a sensitized model we performed a dominant unbiased genome-wide N-ethyl-N-nitrosourea (ENU) mutagenesis screen followed by whole genome sequencing (WGS). We used survival studies, laser-mediated endothelial injury, and ex vivo protein assays to validate hits. ResultsENU-treated at3+/- males were crossed with at3+/- females to produce 4,030 total offspring (1.5x genome coverage). Four permanent lines transmitting a survival benefit beyond 7 months were identified and sequenced. A candidate screen of 63 known coagulation-related loci revealed a missense mutation, C504F, in a highly conserved residue of the prothrombin (F2) heavy chain, which was validated through genetic and biochemical studies. Evaluation of UK Biobank electronic health record (EHR) data was underpowered to detect interactions between F2 and AT3 due to minmal deleterious mutations. Mutations produced through genome editing revealed that heterozygosity for factor X and plasminogen also modified at3-/-, resulting in reduced lethality. The three remaining lines had no coagulation-related variants segregating with survival, suggesting the presence of novel modifier loci. ConclusionsUnbiased genome-wide screening identified a modifier of thrombosis. This demonstrated that re-balancing of hemostasis to mitigate thrombosis is conserved in zebrafish, including an unexpected role for fibrinolysis. This interaction was not detected even in a large human dataset, establishing the continued benefit of the zebrafish model. Finally, we found evidence for novel loci outside of the canonical coagulation cascade that may be new targets for diagnosis or treatment.

cell biology↗

bioRxiv2025

Dabigatran prevents lipopolysaccharide mediated apoptosis in zebrafish through a thrombin independent mechanism

Endotoxemia is a feature of sepsis pathogenesis and has also been found to mediate the pathophysiology of multiple inflammatory conditions. In this work, we use a lipopolysaccharide (LPS) induced endotoxemia model in zebrafish to identify novel mediators of LPS toxicity. We performed transcriptomic studies on LPS-treated larvae, followed by in silico analysis, which revealed associations between the signatures of LPS-treated embryos and those of drugs involving diverse pathways. In parallel, we performed an in vivo screen using >1,500 FDA-approved compounds and identified multiple novel small molecules that reduced inflammation and prevented LPS toxicity. We focused on the direct thrombin inhibitor dabigatran, which was identified through both the in vivo and in silico analyses. We found that dabigatran co-administration significantly reduced the expression of inflammatory cytokines and completely protected zebrafish from endotoxemic death due to LPS. Surprisingly, we found that this protection occurs in prothrombin mutant fish, proving that protection from endotoxemia occurs independently of the anticoagulant function of dabigatran. We additionally found that dabigatran administration significantly decreased nitric oxide production and apoptosis compared to LPS treatment alone, suggesting possible mechanisms by which protection from endotoxemia is achieved. In summary, we identify several novel small molecules that prevent LPS-induced endotoxemia and show that one such small molecule, dabigatran, exerts a thrombin-independent effect on nitric oxide production and apoptosis. This and the other identified small molecules warrant further exploration in inflammatory conditions including sepsis.

pharmacology and toxicology↗

bioRxiv2025

FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

Venous thromboembolism (VTE) is a highly prevalent medical condition with limited therapeutic options and an incomplete understanding of its acquired and inherited subtypes. The zebrafish is a model with the benefits of external development, fecundity, optical transparency, and hemostasis that demonstrates conservation with mammals. We utilized zebrafish as a phenotypic screening tool to identify novel therapeutic options for preventing VTE. A library of FDA-approved compounds was screened for suppression of acquired (elevated estrogen) and spontaneous (protein C deficiency) thrombosis. We found that thyroid hormone, receptor tyrosine kinase (RTK) inhibitors, and proton-pump inhibitors (PPIs) effectively modulated levels of thrombosis, particularly in the estrogen-induced model. These also showed a more favorable hemostatic profile than standard therapies, suggesting alternative mechanisms. Genome editing of thyroid hormone receptor proved that thyroid hormone action is on target. A retrospective electronic health record (EHR) analysis found that thyroid-hormone prescriptions in hormonal contraceptive users correlated with a higher VTE risk, potentially limiting direct repurposing but highlighting thyroid signaling as a pathway involved in estrogen-induced thrombosis. Together, these data identify several drug classes that can be tailored to specific subtypes of VTE and help elucidate distinct pathways driving thrombosis.

pharmacology and toxicology↗

bioRxiv2024

Hormone-induced thrombosis is mediated through non-canonical fibrin(ogen) aggregation and a novel estrogen target in zebrafish

Venous thrombosis is a well-known complication of estrogen exposure, with nearly every woman at risk across her lifetime through contraception, pregnancy, or hormone therapy. Although estrogens alter expression of coagulation factors, the mechanisms that mediate estrogen-induced thrombosis are poorly understood, partially due to the absence of an animal model. Identification of these mediators is central to understanding of hormone-induced pathophysiology, could ascertain patients at higher risk for thrombosis, and pinpoint future therapeutic targets. The zebrafish is characterized by external development, high fecundity, optical transparency, and hemostasis is highly conserved with humans. Through a transgenic line that generates GFP-tagged fibrinogen, we show rapid onset of thrombosis after exposure to various estrogens, but not progestins or testosterone. Thrombi are localized to the venous system with evidence for clot contraction. Thrombosis is only partially impeded by anticoagulants, occurs in the absence of factor VII, factor X, and prothrombin, but is dependent on tissue factor and fibrin(ogen). Finally, targeting of all known estrogen receptors does not eliminate thrombosis. The inability to completely inhibit thrombosis through genetic/pharmacologic anticoagulation or estrogen receptor disruption suggests mechanisms different from canonical coagulation/thrombosis. These studies suggest that estrogen-induced thrombosis is a unique entity distinct from other forms of venous thrombosis.

pathology↗

bioRxiv2024

Loss of factor VIII in zebrafish rebalances antithrombin deficiency but has a limited bleeding diathesis

Deficiencies in coagulation factor VIII (FVIII, F8) result in the bleeding disorder hemophilia A. An emerging novel therapeutic strategy for bleeding disorders is to enhance hemostasis by limiting natural anticoagulants, such as antithrombin (AT3). To study pro/anticoagulant hemostatic balance in an in vivo model, we used genome editing to create null alleles for f8 and von Willebrand factor (vwf) in zebrafish, a model organism with a high degree of homology to the mammalian hemostatic system and unique attributes, including external development and optical transparency. f8 homozygous mutant larvae surprisingly formed normal thrombi when subjected to laser-mediated endothelial injury, had no overt signs of hemorrhage, but had a modest increase in mortality. We have previously shown that at3-/- larvae develop disseminated intravascular coagulation (DIC), with spontaneous thrombosis and fibrinogen consumption, resulting in bleeding phenotype marked by secondary lack of induced thrombus formation upon endothelial injury. We found that with loss of FVIII (f8-/-;at3-/-), larvae no longer developed spontaneous fibrin thrombi and did produce clots in response to endothelial injury. However, homozygous loss of zebrafish Vwf failed to rescue the at3 DIC phenotype. These studies demonstrate an altered balance of natural anticoagulants that mitigates FVIII deficiency in zebrafish, similar to human clinical pipeline products. The data also suggest that zebrafish FVIII might circulate independently of Vwf. Further study of this unique balance could provide new insights for management of hemophilia A and von Willebrand disease. Key Points{square} Zebrafish demonstrate a unique balance of natural anticoagulants that mitigates severe FVIII deficiency. {square}Zebrafish FVIII appears to circulate independently of Vwf, which could have implications for management of hemophilia A.

genetics↗