Search bioRxivSearch

Biology subjects

Bakker, B. M.

Publications and source records attributed to Bakker, B. M..

2 recordsLinked to original sources

Agent-Based Modeling Predicts HDL-independent Pathway of Removal of Excess Surface Lipids from Very Low Density Lipoprotein

A hallmark of the metabolic syndrome is low HDL-cholesterol coupled with high plasma triglycerides (TG), but it is unclear what drives this close association. Plasma triglycerides and HDL cholesterol are thought to communicate through two distinct mechanisms. Firstly, excess surface lipids from VLDL released during lipolysis are transferred to HDL, thereby contributing to HDL directly but also indirectly through providing substrate for LCAT. Secondly, high plasma TG increases clearance of HDL through core-lipid exchange between VLDL and HDL via CETP and subsequent hydrolysis of the TG in HDL, resulting in smaller HDL and thus increased clearance rates.\n\nTo test our understanding of how high plasma TG induces low HDL-cholesterol, making use of established knowledge, we developed a comprehensive agent-based model of lipoprotein metabolism which was validated using monogenic disorders of lipoprotein metabolism.\n\nBy perturbing plasma TG in the model, we tested whether the current theoretical framework reproduces experimental findings. Interestingly, while increasing plasma TG through simulating decreased lipolysis of VLDL resulted in the expected decrease in HDL cholesterol, perturbing plasma TG through simulating increased VLDL production rates did not result in the expected HDL-TG relation at physiological lipid fluxes. However, model perturbations and experimental findings can be reconciled if we assume a pathway removing excess surface-lipid from VLDL that does not contribute to HDL cholesterol ester production through LCAT. In conclusion, our model simulations suggest that excess surface lipid from VLDL is cleared in part independently from HDL.\n\nAuthor summaryWhile it has long been known that high plasma triglycerides are associated with low HDL cholesterol, the reason for this association has remained unclear. One of the proposed mechanisms is that during catabolism of VLDL, lipoproteins rich in triglyceride, the excess surface of these particles become a source for the production of HDL cholesterol, and that therefore decreased catabolism of VLDL will lead to both higher plasma triglyceride and low HDL cholesterol. Another proposed mechanism is that during increased production of VLDL, there will be increased exchange of core lipids between VLDL and HDL, with subsequent hydrolysis of the triglyceride in HDL, leading to smaller HDL that is cleared more rapidly. To investigate these mechanisms further we developed a computational model based on established knowledge concerning lipoprotein metabolism and validated the model with known findings in monogenetic disorders. Upon perturbing the plasma triglycerides within the model by increasing the VLDL production rate, we unexpectedly found an increase in both triglyceride and HDL cholesterol. However, upon assuming that less excess surface lipid is available to HDL, HDL decreases in response to increased VLDL production. We therefore propose that there must be a pathway removing excess surface lipids that is independent from HDL.\n\nAbbreviations

systems biology

Cofactors revisited - predicting the impact of flavoprotein-related diseases on a genome scale

Flavin adenine dinucleotide (FAD) and its precursor flavin mononucleotide (FMN) are redox cofactors that are required for the activity of more than hundred human enzymes. Mutations in the genes encoding these proteins cause severe phenotypes, including a lack of energy supply and accumulation of toxic intermediates. Ideally, patients should be diagnosed before they show symptoms so that treatment and/or preventive care can start immediately. This can be achieved by standardized newborn screening tests. However, many of the flavin-related diseases lack appropriate biomarker profiles. Genome-scale metabolic models can aid in biomarker research by predicting altered profiles of potential biomarkers. Unfortunately, current models, including the most recent human metabolic reconstructions Recon and HMR, typically treat enzyme-bound flavins incorrectly as free metabolites. This in turn leads to artificial degrees of freedom in pathways that are strictly coupled. Here, we present a reconstruction of human metabolism with a curated and extended flavoproteome. To illustrate the functional consequences, we show that simulations with the curated model - unlike simulations with earlier Recon versions - correctly predict the metabolic impact of multiple-acyl-CoA-dehydrogenase deficiency as well as of systemic flavin-depletion. Moreover, simulations with the new model allowed us to identify a larger number of biomarkers in flavoproteome-related diseases, without loss of accuracy. We conclude that adequate inclusion of cofactors in constraint-based modelling contributes to higher precision in computational predictions.

systems biology