Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient

BioModels Parameters: a treasure trove of parameter values from published systems biology models

MOTIVATION

One of the major bottlenecks in building systems biology models is identification and estimation of model parameters for model calibration. Searching for model parameters from published literature and models is an essential, yet laborious task.

RESULTS

We have developed a new service, BioModels Parameters, to facilitate search and retrieval of parameter values from the Systems Biology Markup Language models stored in BioModels. Modellers can now directly search for a model entity (e.g. a protein or drug) to retrieve the rate equations describing it; the associated parameter values (e.g. degradation rate, production rate, Kcat, Michaelis-Menten constant, etc.) and the initial concentrations. Currently, BioModels Parameters contains entries from over 84,000 reactions and 60 different taxa with cross-references. The retrieved rate equations and parameters can be used for scanning parameter ranges, model fitting and model extension. Thus, BioModels Parameters will be a valuable service for systems biology modellers.

AVAILABILITY AND IMPLEMENTATION

The data are accessible via web interface and API. BioModels Parameters is free to use and is publicly available at https://www.ebi.ac.uk/biomodels/parameterSearch.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A biomathematical model of human erythropoiesis and iron metabolism

Anaemia therapy or perisurgical support of erythropoiesis often require both, EPO and iron medication. However, excessive iron medication can result in iron overload and it is challenging to control haemoglobin levels in a desired range. To support this task, we develop a biomathematical model to simulate EPO- and iron medication in humans. We combine our previously established model of human erythropoiesis including comprehensive pharmacokinetic models of EPO applications with a newly developed model of iron metabolism including iron supplementation. Equations were derived by translating known biological mechanisms into ordinary differential equations. Qualitative model behaviour is studied in detail considering a variety of interventions such as bleeding, iron malnutrition and medication. The model can explain time courses of erythrocytes, reticulocytes, haemoglobin, haematocrit, red blood cells, EPO, serum iron, ferritin, transferrin saturation, and transferrin under a variety of scenarios including EPO and iron application into healthy volunteers or chemotherapy patients. Unknown model parameters were determined by fitting the predictions of the model to time series data from literature. We demonstrate how the model can be used to make predictions of untested therapy options such as cytotoxic chemotherapy supported by iron and EPO. Following our ultimate goal of establishing a model of anaemia treatment in chronic kidney disease, we aim at translating our model to this pathological condition in the near future.

Association of serum ferritin with metabolic syndrome in eight cities in China

Objective

This study aims to evaluate the cross‐sectional association of serum ferritin (SF) and the risk of metabolic syndrome (MetS) and its components among adults in eight cities in China.

Methods

Subjects were recruited using a combination of systematic cluster random sampling and purposive sampling in eight cities in China. The sociodemographic characteristics, data of lifestyle factors, self‐reported disease history, and 24‐hr dietary intake were obtained using a validated questionnaire. Anthropometry was performed, and fasting blood was collected to test the SF, fasting blood glucose (FBG), insulin, high‐sensitivity C‐reactive protein (hs‐CRP), triglycerides (TG), and cholesterols. Logistic and linear regression analyses were conducted to investigate the associations, adjusting for age, city level, smoking, drinking, weekly moderate‐to‐vigorous activity, dietary factors, hs‐CRP, and BMI.

Results

Serum ferritin level is positively correlated with total cholesterol, TG, FBG, HOMA‐IR, and hs‐CRP after adjusting for age and BMI. The odds ratio (OR) for MetS in the highest quartile of SF was 2.23 (1.32, 3.77) after adjusting for men, compared with the lowest quartile. An elevated ferritin concentration was significantly related to hypertriglyceridemia (p < .001) and elevated glucose (p = .013) among men, but not among women. Furthermore, compared with Q1, the OR for insulin resistance in the ferritin Q4 group was 3.08 (1.50, 6.32) among men and 1.96 (1.19, 3.24) among women.

Conclusion

A positive association between elevated SF and MetS and its components including hypertriglyceridemia and elevated glucose was found in multivariate analyses among men, and SF levels are independently associated with IR.

Animal Models of Normal and Disturbed Iron and Copper Metabolism

Research on the interplay between iron and copper metabolism in humans began to flourish in the mid-20th century, and diseases associated with dysregulated homeostasis of these essential trace minerals are common even today. Iron deficiency is the most frequent cause of anemia worldwide, leading to significant morbidity, particularly in developing countries. Iron overload is also quite common, usually being the result of genetic mutations which lead to inappropriate expression of the iron-regulatory hormone hepcidin. Perturbations of copper homeostasis in humans have also been described, including rare genetic conditions which lead to severe copper deficiency (Menkes disease) or copper overload (Wilson disease). Historically, the common laboratory rat (Rattus norvegicus) was the most frequently utilized species to model human physiology and pathophysiology. Recently, however, the development of genetic-engineering technology combined with the worldwide availability of numerous genetically homogenous (i.e., inbred) mouse strains shifted most research on iron and copper metabolism to laboratory mice. This created new opportunities to understand the function of individual genes in the context of a living animal, but thoughtful consideration of whether mice are the most appropriate models of human pathophysiology was not necessarily involved. Given this background, this review is intended to provide a guide for future research on iron- and copper-related disorders in humans. Generation of complementary experimental models in rats, swine, and other mammals is now facile given the advent of newer genetic technologies, thus providing the opportunity to accelerate the identification of pathogenic mechanisms and expedite the development of new treatments to mitigate these important human disorders.

Oral Gavage of Ginger Nanoparticle-Derived Lipid Vectors Carrying Dmt1 siRNA Blunts Iron Loading in Murine Hereditary Hemochromatosis

Nanoparticles (NPs) have been utilized to deliver drugs to the intestinal epithelium in vivo. Moreover, NPs derived from edible plants are less toxic than synthetic NPs. Here, we utilized ginger NP-derived lipid vectors (GDLVs) in a proof-of-concept investigation to test the hypothesis that inhibiting expression of divalent metal-ion transporter 1 (Dmt1) would attenuate iron loading in a mouse model of hereditary hemochromatosis (HH). Initial experiments using duodenal epithelial organ cultures from intestine-specific Dmt1 knockout (KO) (Dmt1int/int) mice in the Ussing chamber established that Dmt1 is the only active iron importer during iron-deficiency anemia. Further, when Dmt1int/int mice were crossed with mice lacking the iron-regulatory hormone, hepcidin (Hepc-/-), iron loading was abolished. Hence, intestinal Dmt1 is required for the excessive iron absorption that typifies HH. Additional experiments established a protocol to produce GDLVs carrying functional Dmt1 small interfering RNAs (siRNAs) and to target these gene delivery vehicles to the duodenal epithelium in vivo (by incorporating folic acid [FA]). When FA-GDLVs carrying Dmt1 siRNA were administered to weanling Hepc-/- mice for 16 days, intestinal Dmt1 mRNA expression was attenuated and tissue iron accumulation was blunted. Oral delivery of functional siRNAs by FA-GDLVs is a suitable therapeutic approach to mitigate iron loading in murine HH.

A computational model to understand mouse iron physiology and disease

It is well known that iron is an essential element for life but is toxic when in excess or in certain forms. Accordingly there are many diseases that result directly from either lack or excess of iron. Yet many molecular and physiological aspects of iron regulation have only been discovered recently and others are still elusive. There is still no good quantitative and dynamic description of iron absorption, distribution, storage and mobilization that agrees with the wide array of phenotypes presented in several iron-related diseases. The present work addresses this issue by developing a mathematical model of iron distribution in mice calibrated with ferrokinetic data and subsequently validated against data from mouse models of iron disorders, such as hemochromatosis, β-thalassemia, atransferrinemia and anemia of inflammation. To adequately fit the ferrokinetic data required inclusion of the following mechanisms: a) transferrin-mediated iron delivery to tissues, b) induction of hepcidin by transferrin-bound iron, c) ferroportin-dependent iron export regulated by hepcidin, d) erythropoietin regulation of erythropoiesis, and e) liver uptake of NTBI. The utility of the model to simulate disease interventions was demonstrated by using it to investigate the outcome of different schedules of transferrin treatment in β-thalassemia.

Iron is an essential nutrient in almost all life forms. In humans and animals iron is used for respiration and for transporting oxygen inside red blood cells. But in excess iron can be toxic and therefore the body regulates its distribution and absortion through the action of hormones, which is not yet completely understood. Here we created a computational model of the regulation of iron distribution in the body of a mouse based on experimental data. The model can accurately simulate many iron diseases such as anemia, hemochromatosis, and thalassemia. This computational model is helpful to understand the basis of these diseases and plan therapies to address them.

Gastrointestinal iron excretion and reversal of iron excess in a mouse model of inherited iron excess

The current paradigm in the field of mammalian iron biology states that body iron levels are determined by dietary iron absorption, not by iron excretion. Iron absorption is a highly regulated process influenced by iron levels and other factors. Iron excretion is believed to occur at a basal rate irrespective of iron levels and is associated with processes such as turnover of intestinal epithelium, blood loss, and exfoliation of dead skin. Here we explore iron excretion in a mouse model of iron excess due to inherited transferrin deficiency. Iron excess in this model is attributed to impaired regulation of iron absorption leading to excessive dietary iron uptake. Pharmacological correction of transferrin deficiency not only normalized iron absorption rates and halted progression of iron excess but also reversed body iron excess. Transferrin treatment did not alter the half-life of ⁵⁹Fe in mutant mice. ⁵⁹Fe-based studies indicated that most iron was excreted via the gastrointestinal tract and suggested that iron-loaded mutant mice had increased rates of iron excretion. Direct measurement of urinary iron levels agreed with ⁵⁹Fe-based predictions that urinary iron levels were increased in untreated mutant mice. Fecal ferritin levels were also increased in mutant mice relative to wild-type mice. Overall, these data suggest that mice have a significant capacity for iron excretion. We propose that further investigation into iron excretion is warranted in this and other models of perturbed iron homeostasis, as pharmacological targeting of iron excretion may represent a novel means of treatment for diseases of iron excess.

No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases

Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.