Patil Nitin, Mirveis Zohreh, Byrne Hugh J
FOCAS Research Institute, TU Dublin, Ireland.
School of Physics, Optometric and Clinical Sciences, TU Dublin, Ireland.
FEBS Open Bio. 2024 Mar;14(3):466-486. doi: 10.1002/2211-5463.13765. Epub 2024 Jan 12.
This study aims to demonstrate the benefits of augmenting commercially available, real-time, in vitro glycolysis assays with phenomenological rate equation-based kinetic models, describing the contributions of the underpinning metabolic pathways. To this end, a commercially available glycolysis assay, sensitive to changes in extracellular acidification (extracellular pH), was used to derive the glycolysis pathway kinetics. The pathway was numerically modelled using a series of ordinary differential rate equations, to simulate the obtained experimental results. The sensitivity of the model to the key equation parameters was also explored. The cellular glycolysis pathway kinetics were determined for three different cell-lines, under nonmodulated and modulated conditions. Over the timescale studied, the assay demonstrated a two-phase metabolic response, representing the differential kinetics of glycolysis pathway rate as a function of time, and this behaviour was faithfully reproduced by the model simulations. The model enabled quantitative comparison of the pathway kinetics of three cell lines, and also the modulating effect of two known drugs. Moreover, the modelling tool allows the subtle differences between different cell lines to be better elucidated and also allows augmentation of the assay sensitivity. A simplistic numerical model can faithfully reproduce the differential pathway kinetics for three different cell lines, with and without pathway-modulating drugs, and furthermore provides insights into the cellular metabolism by elucidating the underlying mechanisms leading to the pathway end-product. This study demonstrates that augmenting a relatively simple, real-time, in vitro assay with a model of the underpinning metabolic pathway provides considerable insights into the observed differences in cellular systems.
本研究旨在证明，用基于现象学速率方程的动力学模型增强市售的实时体外糖酵解测定法的益处，该模型描述了基础代谢途径的贡献。为此，使用了一种对细胞外酸化（细胞外pH值）变化敏感的市售糖酵解测定法来推导糖酵解途径动力学。使用一系列常微分速率方程对该途径进行数值建模，以模拟获得的实验结果。还探讨了模型对关键方程参数的敏感性。在未调节和调节条件下，测定了三种不同细胞系的细胞糖酵解途径动力学。在所研究的时间尺度上，该测定法显示出两阶段代谢反应，代表了糖酵解途径速率随时间变化的差异动力学，并且模型模拟忠实地再现了这种行为。该模型能够对三种细胞系的途径动力学以及两种已知药物的调节作用进行定量比较。此外，该建模工具能够更好地阐明不同细胞系之间的细微差异，还能提高测定法的灵敏度。一个简单的数值模型可以忠实地再现三种不同细胞系在有或没有途径调节药物情况下的差异途径动力学，并且通过阐明导致途径终产物的潜在机制，进一步深入了解细胞代谢。本研究表明，用基础代谢途径模型增强相对简单的实时体外测定法，能够深入了解细胞系统中观察到的差异。
