Systems Analysis of Temozolomide Resistance in Glioblastoma Cells

Glioblastoma (GBM), the most aggressive form of brain cancer, remains a major clinical challenge due to its intrinsic heterogeneity and the rapid emergence of resistance against the frontline drug temozolomide (TMZ). To dissect the molecular and metabolic determinants of TMZ response, we characterised resistant and sensitive subpopulations derived from the U87MG cell line using an integrated multi-omics approach, including whole-exome sequencing, microRNA profiling, metabolic phenotyping, and respiration analysis. These datasets were contextualised within a tissue-specific flux balance model of human metabolism to unravel pathway-level rewiring. Our findings reveal that TMZ-resistant cells exhibit glutamine dependence mediated by mutations in signalling pathways regulating central metabolism, alongside differential remodelling of cholesterol metabolism and oxidative phosphorylation. Constraint-based flux sampling and synthetic lethal predictions further identified candidate metabolic vulnerabilities unique to resistant states. This integrative framework underscores the power of systems approaches with special focus on genome-scale metabolic models in capturing tumour heterogeneity, predicting drug response, and guiding the development of personalised therapeutic strategies for GBM.