Abstract
BackgroundSphingolipids play important roles in cell structure and function as well as in the pathophysiology of many diseases. Many of the intermediates of sphingolipid biosynthesis are highly bioactive and sometimes have antagonistic activities, for example, ceramide promotes apoptosis whereas sphingosine-1-phosphate can inhibit apoptosis and induce cell growth; therefore, quantification of the metabolites and modeling of the sphingolipid network is imperative for an understanding of sphingolipid biology.ResultsIn this direction, the LIPID MAPS Consortium is developing methods to quantitate the sphingolipid metabolites in mammalian cells and is investigating their application to studies of the activation of the RAW264.7 macrophage cell by a chemically defined endotoxin, Kdo2-Lipid A. Herein, we describe a model for the C16-branch of sphingolipid metabolism (i.e., for ceramides with palmitate as the N-acyl-linked fatty acid, which is selected because it is a major subspecies for all categories of complex sphingolipids in RAW264.7 cells) integrating lipidomics and transcriptomics data and using a two-step matrix-based approach to estimate the rate constants from experimental data. The rate constants obtained from the first step are further refined using generalized constrained nonlinear optimization. The resulting model fits the experimental data for all species. The robustness of the model is validated through parametric sensitivity analysis.ConclusionsA quantitative model of the sphigolipid pathway is developed by integrating metabolomics and transcriptomics data with legacy knowledge. The model could be used to design experimental studies of how genetic and pharmacological perturbations alter the flux through this important lipid biosynthetic pathway.
Highlights
Sphingolipids play important roles in cell structure and function as well as in the pathophysiology of many diseases
SL in essentially every subcategory, from the lipid backbones [3] to complex SL [4], are highly bioactive and play important roles in diseases [5,6]; methods for “lipidomic” analysis of SL and SL metabolism are important for an in-depth understanding of these enigmatic compounds
The de novo biosynthesis of SL begins with production of the sphingoid base, which utilizes serine and palmitoyl-coenzyme A (CoA) and various fatty acyl-CoAs to make N-acylsphinganines that are desaturated to Cer (N-acylsphingosines) and incorporated into more complex SL such as ceramide 1phosphate (CerP), sphingomyelin (SM), glucosyl- and galactosyl-ceramide (GlcCer and GalCer) and more complex glycosphingolipids [2,11]
Summary
Sphingolipids play important roles in cell structure and function as well as in the pathophysiology of many diseases. Sphingolipids (SL) are categorized as lipids with a sphingoid base backbone [1] that is often derivatized with an amide-linked fatty acid to make ceramides (Cer) and more structurally complex SL with diverse biological functions [2]. The goal of the work presented here is to develop a predictive kinetic model for SL metabolism using the lipidomics and transcriptomics data from the LIPID MAPS studies. This manuscript is organized as follows: we first briefly discuss the experimental data preprocessing and the methodology used for estimating the rate parameters, we present the results of parameter estimation, followed by discussion and conclusions
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
