Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics

Use of methotrexate (MTX), a widely used anti-cancer drug which targets primarily dihydrofolate reductase (DHFR) in the folate pathway is being limited by the emergence of resistance. Despite a large number of studies, a quantitative understanding of target pathway dynamics in resistant cancers is majorly lacking. In this work, we integrated gene expression data from different MTX-resistant cancer cell lines into kinetic models to study dynamics of the folate metabolic pathway. Given that all cell lines are derived from human cancers, the pathway is essentially the same consisting of 11 reactions catalyzed by the same set of enzymes and 1 non-enzymatic reaction. Kinetic models emulating pathway dynamics in MTX-untreated, MTX-treated-sensitive and MTX-treated-resistant conditions were generated and model behaviour at steady state was analysed with respect to concentrations of six folate metabolites and fluxes through the 12 reactions. We observed differences in steady-state properties across these cell lines even in the absence of MTX inhibition. More interestingly, the response of sensitive and resistant variants of each cancer type was also seen to vary in simulations of MTX-inhibition. However, accumulation of dihydrofolate at steady state for all sensitive cell lines along and a decrease towards normal levels for their resistant counterparts remained a common feature in most cases. Metabolic control analysis performed to identify crucial flux controlling elements in the pathway indicated that the enzymes methenyltetrahydrofolate cyclohydrolase (MTCH) and phosphoribosylglycinamide formyltransferase (PGT) could be targeted in combination with DHFR in MTX-resistant cancers for improved therapy.