Bioinformatic and clinical experimental assay uncovers resistance and susceptibility mechanisms of human glioblastomas to temozolomide and identifies new combined and individual survival biomarkers outperforming promoter methylation

Abstract

Background: Glioblastoma (GBM) is the most aggressive and lethal central nervous system (CNS) tumor. The treatment strategy is mainly surgery and/or radiation therapy, both combined with adjuvant temozolomide (TMZ) chemotherapy. Historically, methylation of MGMT gene promoter is used as the major biomarker predicting individual tumor response to TMZ. Objectives: This research aimed to analyze genes and molecular pathways of DNA repair as biomarkers for sensitivity to TMZ treatment in GBM using updated The Cancer Genome Atlas (TCGA) data and validate the results on experimental datasets. Methods: Survival analysis of GBM patients under TMZ therapy and hazard ratio (HR) calculation were used to assess all putative biomarkers on World Health Organization CNS5 reclassified TCGA project collection of molecular profiles and experimental multicenter GBM patient cohort. Pathway activation levels were calculated for 38 DNA repair pathways. TMZ sensitivity pathway was reconstructed using a human interactome model built using pairwise interactions extracted from 51,672 human molecular pathways. Results: We found that expression/activation levels of seven and six emerging gene/pathway biomarkers served as high-quality positive (HR 1.63), respectively, patient survival biomarkers performing better than MGMT methylation. Positive survival biomarkers were enriched in the processes of ATM-dependent checkpoint activation and cell cycle arrest whereas negative—in excision DNA repair. We also built and characterized gene pathways which were informative for GBM patient survival following TMZ administration (HR 0.18–0.44, p < 0.0009; area under the curve 0.68–0.9). Conclusion: In this study, a comprehensive analysis of the expression of 361 DNA repair genes and activation levels of 38 DNA repair pathways revealed 13 potential survival biomarkers with increased prognostic potential compared to MGMT methylation. We algorithmically reconstructed the TMZ sensitivity pathway with strong predictive capacity in GBM.