Ensemble kinetic modelling links residual enzyme activity to clinical symptoms in mitochondrial β-oxidation defects

Abstract

The mitochondrial fatty acid {beta}-oxidation (mFAO) is an important source of energy when carbohydrate stores are depleted. It is also involved in many diseases, including inherited fatty-acid oxidation deficiencies (mFAODs). Patients with the same genetic variant often present with clinically heterogeneous phenotypes, but the mechanisms contributing to this heterogeneity are poorly understood. To investigate the underlying pathophysiology of different mFAODs, we constructed a computational model of mFAO in human liver, based on experimentally determined enzyme kinetics. A recognised, but seldom addressed challenge in metabolic modelling is the substantial uncertainty about kinetic parameter values. Whereas experimental values of some mFAO parameters are quite reproducible, others vary by up to four orders of magnitude between different reports. To address this, we generated an ensemble of kinetic models, each with the same reaction stoichiometry and rate equations, but different kinetic parameters, sampled from distributions of literature-derived values. We also comprehensively report these values and the arguments based on which they were evaluated. The resulting models were validated against available flux data, yielding a final ensemble of 51 valid models. These models recapitulate recent findings about the accumulation of medium-chain acyl-CoAs and the concomitant depletion of free CoA (CoASH) in medium-chain acyl-CoA dehydrogenase deficiency. We applied the ensemble to a set of known mFAODs, separating them into long-chain (LC-) and short-/medium-chain (S/MC-)mFAODs. The residual activity at which clinical symptoms are known to occur corresponded well with the residual activity in the model at which pathway flux was significantly decreased in LC-mFAODs. Residual activity in S/MC-mFAODs correlated less strongly with pathway flux, but these deficiencies did show a combined flux- and CoASH-reduction effect. This comparison is of importance to researchers and clinicians, as it identifies possible ways in which insights about one mFAOD may be applied to another based on shared biochemical properties. Author SummaryWhen building computer models of metabolic pathways, it is typical to take the "best" experimental data and use that as input into the model. However, especially when working with human cells, ethical and practical constraints often mean that even the "best" experimental data is still subject to substantial uncertainty. We explicitly modelled the uncertainty about the inner workings of fat burning (fatty acid oxidation). The resulting model is known as an "ensemble". The ensemble predicts ranges instead of single outcomes, allowing us to assess the confidence level of our predictions. We assess a set of inherited diseases - enzyme deficiencies - simulating them at different levels of severity with the ensemble. We find that the model does a good job of predicting the severity of the deficiencies at which symptoms will occur. It also allows us to identify a key difference between two subgroups within this group of deficiencies: long-chain and medium-/short-chain, depending on the size of the fats being metabolised. The long-chain variant is predicted to correlate most straightforwardly with the severity of the deficiencies, due to its effect on energy generation. Medium-/short-chain deficiencies, in contrast, have more complex consequences.