Biology subjects

Oldenburg, J.

Publications and source records attributed to Oldenburg, J..

8 recordsLinked to original sources

bioRxiv2026

Vitamin K2 Limits Ferroptosis-Associated Lipid Peroxidation and Attenuates Aortic Valve Stenosis

BackgroundCalcific aortic valve stenosis (AS) is the most common valvular heart disease in the aging population and lacks effective pharmacological therapy. Oxidative stress is a key feature of valvular remodeling, yet the mechanisms linking oxidative injury to calcification remain unclear. Ferroptosis, a lipid peroxidation-driven form of regulated cell death, has emerged as a key mediator of oxidative tissue injury and may contribute to cardiovascular disease. Vitamin K was recently identified as a suppressor of ferroptosis and cardiovascular calcification, but whether ferroptosis links vitamin K status to disease progression in AS remains unknown. Methods and ResultsWe investigated the role of lipid peroxidation and ferroptosis in AS and their modulation by vitamin K2 using a translational approach. In human stenotic aortic valves, lipid peroxidation was markedly increased and localized to calcified regions, consistent with a ferroptosis-associated microenvironment. In primary human valvular interstitial cells (VICs), pro-calcific conditions induced lipid peroxidation and a pro-ferroptotic state. Pharmacological induction of ferroptosis enhanced VIC calcification, whereas its inhibition attenuated mineralization, supporting a causal role in osteogenic remodeling. Impaired vitamin K status was associated with increased valvular lipid peroxidation in AS patients. Conversely, vitamin K2 attenuated lipid peroxidation, preserved cell viability under ferroptotic stress, and partially normalized pro-ferroptotic and inflammatory transcriptional programs in VICs. In a murine model of AS, dietary vitamin K2 supplementation attenuated disease progression, reduced transvalvular gradients, and decreased valvular inflammation and lipid peroxidation-associated pathways. Finally, in a prospective cohort of patients with aortic sclerosis to moderate AS (n = 157), circulating undercarboxylated osteocalcin, a marker of impaired vitamin K status, was independently associated with accelerated disease progression. ConclusionsVitamin K2 counteracts ferroptosis-associated lipid peroxidation in AS and attenuates disease severity in vivo. Impaired vitamin K status is independently associated with accelerated progression in patients. These findings position vitamin K2 as a potential disease-modifying strategy and vitamin K status as a prognostic marker in AS. What Is New?O_LIFerroptotic lipid peroxidation is enriched in calcified regions of human stenotic aortic valves. Pharmacological induction of ferroptosis increases, and its inhibition reduces, calcification of human valvular interstitial cells, indicating a causal contribution to valvular mineralization. C_LIO_LIVitamin K2 suppresses ferroptotic lipid peroxidation, preserves cell viability under ferroptotic stress, and shifts pro-oxidative and pro-inflammatory transcriptional programs in human valvular interstitial cells toward a protective state. C_LIO_LIIn an in vivo model of aortic stenosis, dietary vitamin K2 attenuated hemodynamic progression, with lower peak transvalvular velocity and mean gradient, and reduced valvular inflammation and lipid peroxidation, without affecting coagulation C_LIO_LIIn a prospective cohort of 157 patients with aortic sclerosis to moderate stenosis, impaired vitamin K status, reflected by higher circulating undercarboxylated osteocalcin, was independently associated with accelerated disease progression and with higher rates of mortality. C_LI What Are the Clinical Implications?O_LIAortic stenosis currently has no medical therapy. Vitamin K2, an inexpensive, safe nutrient that does not interfere with anticoagulation, emerges as a candidate disease-modifying strategy that warrants testing in randomized trials. C_LIO_LICirculating undercarboxylated osteocalcin may serve as a biomarker to identify patients at risk of rapid progression and to enrich future vitamin K trials for those most likely to benefit. C_LIO_LITargeting valvular lipid peroxidation, through antioxidant repletion and/or inhibition of lipid-peroxidation enzymes, may be a mechanistically grounded approach to slow calcific aortic valve disease. C_LI

physiology↗

bioRxiv2026

Engineered endothelial cell grafts form functional anastomoses and enable recruitment of intravenously delivered human T cells in CAM tumor models

The development of cancer immunotherapies requires preclinical models that capture intravenous delivery, immune cell recruitment and intratumoral T cell activation. Conventional 3D in vitro systems lack perfused vascular networks, whereas mouse models are limited by throughput. The chick chorioallantoic membrane (CAM) assay enables rapid growth of vascularized tumors derived from human cancer cells in ovo, but its application to human T cell-based immunotherapy testing is constrained by CAM-derived vascularization and species-specific barriers between human immune cells and avian endothelium. Here, we establish an endothelial graft-enhanced CAM tumor model that incorporates an immortalized murine endothelial cell line capable of anastomosing with the chick vasculature. This generates a perfused and branched mammalian vascular interface within human tumor xenografts growing on the CAM. Human ICAM-1 expression on the grafted endothelial cells further enhances recruitment of intravenously delivered human T cells into CAM tumors. Using this platform, we demonstrate target-dependent intratumoral T cell activation by bispecific T cell engagers (TCEs) across tumor models, including evaluation of the clinically approved DLL3-targeting TCE tarlatamab in small cell lung cancer models.

bioengineering↗

bioRxiv2026

Evolutionary algorithms accelerate de novo design of potent Nectin-4-specific cancer biologics

Recent advances in AI-based structural biology have made de novo protein binder design increasingly effective, yet performance remains highly target dependent. For instance, the cancer surface antigen Nectin-4, an immunoglobulin-like cell adhesion protein, proved particularly challenging for RFdiffusion-based minibinder generation, yielding substantially fewer high-quality candidates than related targets. To address this bottleneck, we integrated an evolutionary genetic algorithm (GA) with AI-driven design. GA selection with tunable stringency was coupled with diversification via partial diffusion or direct sequence editing, enabling efficient exploration of sequence-structure space and rapid enrichment of promising candidates. This AI-GA pipeline quickly produced large and diverse minibinder panels with very good in silico quality metrics and is compatible with inputs from multiple design algorithms. Pooled, large-scale experimental screening identified highly stable Nectin-4 minibinders with single-digit nanomolar down to subnanomolar affinities. Lead binders were further engineered into Nectin-4-specific flow cytometry detection reagents and potent bispecific T cell engagers, demonstrating functional activity beyond binding. Together, these results show that evolutionary refinement can unlock challenging targets and accelerate de novo protein design for next-generation cancer biologics.

bioengineering↗

bioRxiv2025

Development of AI-designed protein binders for detection and targeting of cancer cell surface proteins

Artificial intelligence (AI)-based protein design opens new avenues for the rapid generation of new research tools and therapeutics, but experimental validation lags behind the computational design throughput. Here, we present a scalable workflow for the discovery and validation of AI-designed protein binders. Leveraging the RFdiffusion protein design pipeline with a custom filter for stable alpha-helical bundle folds, we construct libraries of thousands of AI-binders against cancer-associated surface proteins. Mammalian cell-surface and phage display screening yield multiple high-affinity PD-L1 binders but fewer hits for CD276 (B7-H3) and VTCN1 (B7-H4), reflecting the target-dependent efficiency of RFdiffusion in generating high-quality designs. Using our experimentally validated AI-designed binder libraries, we benchmark freely available structure prediction models. We find that interface predicted template modelling (ipTM) scores by Chai-1 with ESM embedding correlate well with experimental success and even predict deleterious effects of binding interface mutations. To demonstrate the versatility of AI-binders as research tools, we deploy them in CAR-T cells and also assemble them with fluorophore-labeled streptavidin into tetravalent quattrobinders, which achieve antibody-comparable staining of endogenous PD-L1 by flow cytometry. With high production yields and accessible structural models, AI-designed quattrobinders are versatile and cost-effective research tools amenable to community-driven validation and optimization.

bioengineering↗

bioRxiv2025

NKG7 is a stable marker of cytotoxicity across immune contexts and within the tumor microenvironment

Cytotoxicity is a cornerstone of immune defense, critical for combating tumors and infections. This process relies on the coordinated action of granzymes and pore-forming proteins, with Granzyme B (GZMB) and Perforin (PRF1) being key markers and the most widely studied molecules pertaining to cytotoxicity. However, other human granzymes and cytotoxic components remain underexplored, despite growing evidence of their distinct, context-dependent roles. Natural Killer Cell Granule Protein 7 (NKG7) has recently emerged as a crucial cytotoxicity regulator, yet its expression patterns and function are poorly understood. Using large publicly available single-cell RNA sequencing atlases, we performed a comprehensive profiling of cytotoxicity across immune subsets and tissues. Our analysis highlights NKG7 expression as a strong marker of cytotoxicity, exhibiting a strong correlation with overall cytotoxic activity (r = 0.97) and surpassing traditional markers such as Granzyme B and Perforin in reliability. Furthermore, NKG7 expression is notably consistent across diverse immune subsets and tissues, reinforcing its versatility and robustness as a cytotoxicity marker. These findings position NKG7 as an invaluable tool for evaluating immune responses and a reliable indicator of cytotoxic functionality across biological and clinical contexts.

immunology↗

bioRxiv2023

Coagulation activation-induced fibrinolysis biomarker changes depend on thrombophilic risk factors and their clinical phenotype: an interventional in vivo study

BackgroundRecently we have shown alterations in the anticoagulant response to recombinant activated factor VII (rFVIIa)-induced coagulation activation in patients with thrombophilia. ObjectivesHere we extended this in vivo model to study fibrinolysis biomarkers. MethodsThe study population included 56 patients with thrombophilia and a history of venous thromboembolism (VTE+), 38 asymptomatic patients with thrombophilia (VTE-) and 35 healthy controls. Plasma levels of D-dimer, plasmin-2-antiplasmin complex (PAP), and plasminogen activator inhibitor-1 (PAI-1) were monitored over 8 hours after rFVIIa infusion (15 {micro}g/kg) along with thrombin activation markers and activated protein C (APC). ResultsIn all cohorts, PAP increased (P<3.9{middle dot}10-10) and PAI-1 decreased (P<3.5{middle dot}10-8). In contrast to thrombin-antithrombin complex (TAT), which also increased temporarily in all cohorts (P<3.6{middle dot}10-6), changes of PAP and PAI-1 did not reverse during the observation period. The area under the curve (AUC) of PAP (respectively TAT), as measure of plasmin (respectively thrombin) formation, was greater in the VTE+ cohort than in healthy controls (PAP AUC P=0.003, TAT AUC P=2.5{middle dot}10-4) and showed correlation (r=0.554). As evidenced by the respective AUCs, asymptomatic factor V Leiden (FVL) carriers in the VTE-cohort showed less PAP formation (P=9{middle dot}10-4), more pronounced PAI-1 decline (P=0.010), and increased APC formation (P=0.020) than those within the VTE+ group (n=19 each). This was not observed in prothrombin 20210G>A carriers or patients with unexplained familial thrombophilia. ConclusionrFVIIa-induced thrombin formation is associated with fibrinolysis parameter changes outlasting the concomitant anticoagulant response. Both correlate with thrombosis history in FVL and might help to explain its variable clinical expressivity. EssentialsO_LIImpairment of fibrinolysis might result in increased risk of thrombosis. C_LIO_LIWe studied fibrinolytic biomarkers after coagulation activation by recombinant factor VIIa. C_LIO_LIHereby induced alterations in fibrinolytic biomarkers outlast concomitant anticoagulant changes. C_LIO_LIFactor V Leiden carriers with or without thrombosis showed distinct fibrinolytic changes. C_LI

pathology↗

bioRxiv2023

The Endothelium Modulates the Prothrombotic Phenotype of Factor V Leiden: Evidence from an Ex Vivo Model

BackgroundClinical expressivity of the thrombophilic factor V Leiden (FVL) mutation is highly variable. Increased activated protein C (APC) formation in response to thrombin formation has been observed in asymptomatic FVL carriers in vivo. Here we further explored this association using a recently developed endothelial colony forming cell (ECFC)-based ex-vivo model. MethodsECFCs and citrated plasma were obtained from FVL carriers with/without previous venous thromboembolism (VTE+/-, n=7 each) and seven healthy controls. Coagulation was activated by tissue factor in defibrinated recalcified plasma added to confluent cell cultures. Thrombin and APC concentration were measured over time and the respective areas under the curve (AUC) calculated. Additionally, inhibition kinetics of exogenously added APC and APC sensitivity of the prothrombinase complex were measured in plasma. Expression of thrombomodulin and endothelial protein C receptor (EPCR) on ECFCs was assessed using cell-based enzyme-linked immunosorbent assays. ResultsIn autologous plasma on ECFCs, the APC response to thrombin formation (AUC APC/AUC thrombin), was higher in FVL VTE-than FVL VTE+ patients (0.138 versus 0.028, P=0.026). APC inactivation kinetics, APC sensitivity, and thrombomodulin/EPCR expression on ECFCs did not differ between these cohorts and compared to healthy controls. Cross-over experiments with plasma from FVL VTE- and FVL VTE+ patients on non-FVL ECFCs yielded indistinguishable results. In contrast, in normal plasma on FVL VTE-ECFCs the APC response remained significantly higher than on FVL VTE+ ECFCs (0.052 versus 0.022, P=0.011). ConclusionsConsistent with results from previous in vivo experiments, APC response rates to thrombin formation were higher in asymptomatic FVL carriers compared to those with previous VTE. Our observations suggest that this increased APC response is driven by the endothelium. Further studies are warranted to elucidate yet unknown endothelial mechanisms that might modulate the clinical expressivity of FVL.

pathology↗

bioRxiv2019

The plasma Factor XIII heterotetrameric complex structure: unexpected unequal pairing within a symmetric complex

Factor XIII (FXIII) is a predominant determinant of clot stability, strength, and composition. Plasma FXIII circulates as a pro-transglutaminase with 2 catalytic A subunits and 2 carrier-protective B subunits in a heterotetramer (FXIII-A2B2). FXIII-A2 and -B2 subunits are synthesized separately and then assembled in plasma. Following proteolytic activation by thrombin and calcium-mediated dissociation of the B-subunits, activated FXIII (FXIIIa) covalently cross-links fibrin, promoting clot stability. The zymogen and active states of the FXIII-A subunits have been structurally characterized; however, the structure of FXIII-B subunits and the FXIII-A2B2 complex have remained elusive. Using integrative hybrid approaches including atomic force microscopy, cross-linking mass spectrometry, and computational approaches, we have constructed the first all-atom model of the FXIII-A2B2 complex. We also used molecular dynamic simulations in combination with isothermal titration calorimetry to characterize FXIII-A2B2 assembly, activation, and dissociation. Our data reveal unequal pairing of individual subunit monomers in an otherwise symmetric complex, and suggest this unusual structure is critical for both assembly and activation of this complex. Our findings enhance understanding of mechanisms associating FXIII-A2B2 mutations with disease and have important implications for the rational design of molecules to alter FXIII assembly and/or activity to reduce bleeding and thrombotic complications.

molecular biology↗