Abstract
BACKGROUND: Understanding the complex molecular mechanisms driving drug resistance in glioblastoma (GBM) is crucial to develop effective therapeutic strategies. While prior studies have identified resistance mechanisms tied to specific drugs or pathways, a multi-modal molecular analysis of resistance across a range of drug classes is lacking. METHODS: We identified highly drug-resistant (n = 5) and drug-sensitive (n = 4) cultures from a cohort of 32 patient-derived glioblastoma stem cell (GSC) cultures screened against a broad panel of ~ 500 anti-cancer drugs. To elucidate the key drivers of drug resistance, we performed integrative profiling of stemness, differentiation capacity, global gene expression, mutation profiles, and DNA methylation patterns between the two groups. RESULTS: Despite heterogeneous gene expression profiles, drug-resistant GSCs showed consistent upregulation of ATP-binding cassette (ABC) drug efflux transporters, stemness, and extracellular matrix (ECM)-related genes. Compared to drug-sensitive GSCs, drug-resistant GSCs exhibited more pronounced stem-like properties and reduced differentiation capacity. Notably, genes linked to axonogenesis displayed significant CpG island hypomethylation in drug-resistant GSCs. CONCLUSIONS: This study suggests a pivotal role for GSC plasticity, stemness maintenance, and ECM-mediated drug evasion in GBM treatment resistance. Our findings highlight the adaptive and dynamic nature of resistance mechanisms in GSCs, emphasizing the need for comprehensive molecular insights to inform targeted therapeutic strategies in GBM. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12885-025-15163-z.