The break in the cycle: Inositol pyrophosphate fluxomics disentangled via mathematical modelling

This study investigates the metabolic pathways of inositol pyrophosphates (IPPs) in the yeast cell line ΔSPX and the human tumor cell line HCT116. Utilizing pulse-labelling experiments with ¹⁸ O water and ordinary differential equation (ODE) models, we explore the synthesis and turnover of the highly phosphorylated IPP, 1,5-InsP ₈ . Our findings challenge the notion that 1,5-InsP ₈ can be synthesized through distinct routes, revealing a linear reaction sequence in both systems. Employing model reduction via the profile likelihood method, we achieved statistically concise identifiability analysis that led to significant biological insights. In yeast, we determined that 1,5-InsP ₈ production primarily occurs through the phosphorylation of 5-InsP ₇ , with the pathway involving 1-InsP ₇ deemed unnecessary as its removal did not compromise model accuracy. In HCT116 cells, 1,5-InsP ₈ synthesis is mainly driven by 1-InsP ₇ , with variations observed across different experimental conditions. These results underscore the utility of model reduction in enhancing our understanding of metabolic pathways, challenging traditional views of IPP metabolism, and providing a framework for future investigations into the regulation and implications of linear IPP pathways in eukaryotic cells.