Metabolic Modeling of Dynamic 13C NMR Isotopomer Data in the Brain In Vivo: Fast Screening of Metabolic Models Using Automated Generation of Differential Equations

Abstract

Most current brain metabolic models are not capable of taking into account the dynamic isotopomer information available from fine structure multiplets in 13C spectra, due to the difficulty of implementing such models. Here we present a new approach that allows automatic implementation of multi-compartment metabolic models capable of fitting any number of 13C isotopomer curves in the brain. The new automated approach also makes it possible to quickly modify and test new models to best describe the experimental data. We demonstrate the power of the new approach by testing the effect of adding separate pyruvate pools in astrocytes and neurons, and adding a vesicular neuronal glutamate pool. Including both changes reduced the global fit residual by half and pointed to dilution of label prior to entry into the astrocytic TCA cycle as the main source of glutamine dilution. The glutamate-glutamine cycle rate was particularly sensitive to changes in the model.

Quantitative NMR Studies of Multiple Compound Mixtures

“…NMR technique can offer two different types of information (specific enrichments and isotopic isomers) [99]. Combined with 13 C-labeling, it is often applied to determine metabolic fluxes in biological systems [100,101]. The metabolic flux in complex network can be evaluated from the labeling pattern of metabolites of biological samples incubated with 13 C-labeled substrates.…”

Experimental strategies for in vivo 13 C NMR spectroscopy

“…the amount of 13 C at a given atomic position is quantified irrespective of the labeling at other atomic positions. In direct detection, quantification can also be achieved at the isotopomer level, which in theory provides more information than the sole positional enrichments [41,112]. However, since isotopomer detection relies on scalar 13 C-13 C scalar J-coupling, it is possible only if the linewidth is narrower than J-coupling constant (which is not possible with poor shim, or at very high magnetic field).…”

“…This fine structure can then be connected to bonded cumomers, which represent some classes of isotopomers accessible to 13 C MRS (see Ref. [41] for a detailed explanation of the concept of bonded cumomer and the relation with multiplet structure, and [112,113] for in vivo applications). In any case, this crucial step requires much attention to minimize quantification bias.…”

“…see Ref. [122] for detailed derivation of the bi-compartmental neuron-astrocyte model in the brain, [123] for didactic presentation of model generation and utilization, and [112] for isotopomer modeling and possible refinements of the bi-compartmental model).…”

Astrocytes, Metabolism, Signaling and Brain Drains: Introduction to the Special Issue in Honor of Gerald Dienel

“…[6]. In this issue, Pierre-Gilles Henry has attempted to make model choice a little easier for scientists by describing an automated method for modifying and testing models [7].…”