The intestine is a major source of systemic ammonia (NH3); thus, capturing part of gut NH3 may mitigate disease symptoms in conditions of hyperammonemia such as urea cycle disorders and hepatic encephalopathy. As an approach to the lowering of blood ammonia arising from the intestine, we engineered the orally delivered probiotic Escherichia coli Nissle 1917 to create strain SYNB1020 that converts NH3 to l-arginine (l-arg). We up-regulated arginine biosynthesis in SYNB1020 by deleting a negative regulator of l-arg biosynthesis and inserting a feedback-resistant l-arg biosynthetic enzyme. SYNB1020 produced l-arg and consumed NH3 in an in vitro system. SYNB1020 reduced systemic hyperammonemia, improved survival in ornithine transcarbamylase–deficient spfash mice, and decreased hyperammonemia in the thioacetamide-induced liver injury mouse model. A phase 1 clinical study was conducted including 52 male and female healthy adult volunteers. SYNB1020 was well tolerated at daily doses of up to 1.5 × 1012 colony-forming units administered for up to 14 days. A statistically significant dose-dependent increase in urinary nitrate, plasma 15N-nitrate (highest dose versus placebo, P = 0.0015), and urinary 15N-nitrate was demonstrated, indicating in vivo SYNB1020 activity. SYNB1020 concentrations reached steady state by the second day of dosing, and excreted cells were alive and metabolically active as evidenced by fecal arginine production in response to added ammonium chloride. SYNB1020 was no longer detectable in feces 2 weeks after the last dose. These results support further clinical development of SYNB1020 for hyperammonemia disorders including urea cycle disorders and hepatic encephalopathy.

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Blood function defines bleeding and clotting risks and dictates approaches for clinical intervention. Independent of adding exogenous tissue factor (TF), human blood treated in vitro with corn trypsin inhibitor (CTI, to block Factor XIIa) will generate thrombin after an initiation time (Ti) of 1 to 2 hours (depending on donor), while activation of platelets with the GPVI-activator convulxin reduces Ti to ∼20 minutes. Since current kinetic models fail to generate thrombin in the absence of added TF, we implemented a Platelet-Plasma ODE model accounting for: the Hockin-Mann protease reaction network, thrombin-dependent display of platelet phosphatidylserine, VIIa function on activated platelets, XIIa and XIa generation and function, competitive thrombin substrates (fluorogenic detector and fibrinogen), and thrombin consumption during fibrin polymerization. The kinetic model consisting of 76 ordinary differential equations (76 species, 57 reactions, 105 kinetic parameters) predicted the clotting of resting and convulxin-activated human blood as well as predicted Ti of human blood under 50 different initial conditions that titrated increasing levels of TF, Xa, Va, XIa, IXa, and VIIa. Experiments with combined anti-XI and anti-XII antibodies prevented thrombin production, demonstrating that a leak of XIIa past saturating amounts of CTI (and not “blood-borne TF” alone) was responsible for in vitro initiation without added TF. Clotting was not blocked by antibodies used individually against TF, VII/VIIa, P-selectin, GPIb, protein disulfide isomerase, cathepsin G, nor blocked by the ribosome inhibitor puromycin, the Clk1 kinase inhibitor Tg003, or inhibited VIIa (VIIai). This is the first model to predict the observed behavior of CTI-treated human blood, either resting or stimulated with platelet activators. CTI-treated human blood will clot in vitro due to the combined activity of XIIa and XIa, a process enhanced by platelet activators and which proceeds in the absence of any evidence for kinetically significant blood borne tissue factor.

IntroductionPlaque rupture reveals tissue factor (TF) to flowing blood, resulting in coronary thrombosis and occlusion with consequent acute myocardial infarction. Despite the prevalence of this event, the critical concentration of surface tissue factor required to cause clotting at various hemodynamic conditions remains poorly defined. In addition, the existence, source(s), and functional activity of circulating levels of tissue factor are not fully resolved in health or disease. The function of circulating TF in concert with wallderived TF may depend on prevailing flow conditions. TF in a lipid surface serves as a cofactor for factor VIIa (present at ϳ 1% of the 10-nM factor VII concentration) resulting in approximately 10 5 -fold enhancement of factor Xa formation. 1 Platelet deposition may reduce access of factor X to the TF/VIIa complex formed on the damaged wall. 2,3 Elevated TF antigen and activity are detectable in human atherosclerotic lesions and are expressed by various cell types. 4 Bonderman et al 5 determined, using ex vivo plaque disruption/scraping, that the average TF site density underneath plaques is 33 pg TF/cm 2 , corresponding to approximately 6 molecules-TF/m 2 . Drake et al 6 found that in human cardiac and skeletal muscle the TF levels were 7 and 119 ng TF/mg protein, respectively. Tissue factor pathway inhibitor (TFPI) is also elevated in atherosclerotic vessels in comparison with 10 to 20 ng TFPI/cm 2 in healthy vessels. 7 Blood-borne tissue factor antigen was first reported in a system using 5-minute ex vivo perfusion of human blood over collagencoated slides, 8 a system in which fibrin deposition was blocked by inhibited factor VIIa (FVIIa i ). Collagen-activated platelets are highly procoagulant and may present factor VIIa cofactor activity susceptible to antagonism by antibodies or FVIIa i . 9-11 A recent study of 91 individuals using the Luminex assay (Austin, TX) indicated that most healthy individuals had less than 2 pM TF in plasma, 12 a value lower than the average 4 pM TF obtained from a literature survey of plasma TF levels in healthy individuals measured by enzyme-linked immunosorbent assay (ELISA). Addition of increasing amounts of subpicomolar levels of lipidated TF to corn trypsin inhibitor (CTI)-treated whole blood indicates that active TF in healthy individuals is subpicomolar, estimated to between less than 20 fM 13 and less than 200 fM. 14 Recently, rapid splicing of TF pre-mRNA and expression of TF antigen have been reported in sonicated membranes obtained from activated platelets. 15 Under flow conditions, the transfer of tissue factor may be of importance via leukocyte delivery to platelets via CD15 16 or capture of microparticles presenting TF and PSGL-1 17-19 or derived from platelets. 10 Mathematic simulations of the hemostatic response have also taken into account the importance of tissue factor site density. Kuharsky and Fogelson 3 developed a full transport-reaction coagulation model that takes into account surface-dependent reactions, transport of factors a...

Summary Experimental fibroblast growth factor 21 (FGF21) analogs can improve lipid profiles in patients with metabolic diseases. However, their effects on markers of insulin sensitivity appear to be minimal, potentially because of insufficient exposure. Systemic drug levels vary from sub-pharmacological to demonstrating pharmacodynamic effects but with dose-limiting adverse events. Here we report results from a phase 1 multiple ascending dose study of AKR-001, an Fc-FGF21 fusion protein engineered for sustained systemic pharmacologic exposure, in individuals with type 2 diabetes. With a half-life of 3–3.5 days, the peak-to-trough ratio under steady-state conditions is approximately 2 following QW dosing. AKR-001 appears to demonstrate pharmacodynamic effects on serum markers of insulin sensitivity and acceptable tolerability up to and including 70 mg QW. Positive trends in lipoprotein profile, including triglycerides, non-high-density lipoprotein (non-HDL) cholesterol, HDL-C, and apolipoproteins B and C3 are consistent with other FGF21 analogs. AKR-001’s clinical profile supports further evaluation as a treatment for metabolic diseases.