Temporal multi-omic profiling reveals chemoradiotherapy-specific dualistic metabolic rewiring that supports glioblastoma tumor recurrence (Bulk RNA-Seq)

Tumor recurrence afflicts over 95% of glioblastoma (GBM) patients, contributing to the disease's high fatality rates. To unravel the molecular mechanisms behind post-therapy recurrence, we employed a clinically-relevant chemoradiotherapy model, studying the temporal molecular metabolic evolution of patient-derived GBM samples in vitro and in vivo. Leveraging unbiased multi-omics methods, including single-cell and bulk transcriptomics, untargeted metabolomics, and stable isotope tracing, we revealed a dynamic metabolic rewiring favoring one-way anaplerotic pyruvate metabolism via carboxylation across GBM samples. This conserved adaptation, confirmed in independent datasets, resulted in reduced glucose-derived acetyl-coA production, hindering histone acetylation and silencing neural-differentiation genes NEUROD1 and DCX. Pharmacological intervention targeting this metabolic shift reduced recurrent GBM cell aggressiveness, prolonging survival in preclinical GBM xenograft tumors treated with chemoradiotherapy. These findings illuminate a potential metabolic therapeutic avenue to enhance current strategies, addressing disease recurrence and offering much-needed improvements in survival outcomes for GBM patients suffering from this dismal disease. Overall design: GBM cells received 25 µM of temozolomide and controls received equal volumes of DMSO vehicle. Immediately following TMZ treatment, cells were exposed to 1 Gy of X-ray irradiation using the Rad Source 2000 and incubated at 37°C in a 5% CO2 incubator for 1 hour. To mimic the exposure time of chemotherapy received by patients, where the half-life of TMZ is approximately 1-2 hours in circulation, the drug treatment was washed out of the patient-derived GBM cells after 1 hour and replaced with fresh media. The concurrent chemoradiotherapy treatment regimen was repeated daily for 5 consecutive days. After the 5th treatment day, patient-derived GBM cells received a 2-day treatment holiday prior to collection and subsequent analysis. Chemoradiotherapy naive or TMZRT-resistant GBM cells received 100 µM of UK-5099 or equal volumes of DMSO vehicle. Total RNA samples were submitted for Next Generation sequencing at the UBC Sequencing + Bioinformatics Consortium, Vancouver, BC.