Variations in DNA Repair Genes and Intratumoral Genetic Heterogeneity in Temozolomide-Resistant Glioblastoma

Glioblastoma (GBM) is the most prevalent primary brain tumor. Despite extensive investigations, GBM's resistance to the first-line drug temozolomide (TMZ) remains a major challenge in clinical management. This study explores the molecular mechanisms underlying TMZ resistance in GBM, emphasizing the roles of DNA repair gene polymorphisms and intratumoral genetic heterogeneity.

In this study, we collected 10 matched pairs of GBM surgical samples, including tumor tissues from the first and second surgeries, and proceeded with RNA-Seq and Exome-Seq. We performed pathway enrichment analysis and functional assays for key genetic variations in the DNA repair pathway to establish a mechanistic relationship between genetic changes and drug resistance. Sanger sequencing validated somatic variations before and after chemotherapy, and we analyzed changes in gene expression associated with DNA repair. The methylation status of the promoter region of the MGMT gene was analyzed, in addition to the effect of DNA repair genes on TMZ sensitivity in cells.

This study identified 20 novel somatic mutations that uniquely occurred in pre-TMZ and post-TMZ chemotherapy samples and were significantly related to DNA repair pathways (including base excision repair [BER] and nucleotide excision repair [NER]). Functional validation experiments confirmed that the alterations in the expressed variants had disrupted important repair mechanisms related to the survival of tumor cells. Notably, differential dysregulation of the NER and BER pathways (upregulated NER and inactivated BER) was observed in recurrent tumors, serving as a compensatory mechanism for TMZ resistance. Methylation of the MGMT gene promoter region has been linked to TMZ resistance, while intratumoral genetic heterogeneity might increase the chance of resistance. Importantly, our observations point toward an evolutionary event following TMZ treatment that incorporates selective pressures for repair-deficient clones, resulting in a more aggressive fate for GBM. Cellular studies showed that the proliferation and migration ability of U87 cells were significantly elevated after the knockdown of XAB2, PNKP, and OGG1.

This study represents the first comprehensive characterization of TMZ resistance in GBM based on integrated genetic, epigenetic, and functional validation approaches. In GBM, mechanisms of TMZ resistance are elucidated, with the interplay between the NER and BER pathways (compensatory regulation) being a key mechanism, alongside variations in DNA repair genes and intratumoral genetic heterogeneity. These findings highlight the importance of targeting the crosstalk between NER and BER pathways for GBM therapy, emphasizing the necessity of personalized treatment strategies and suggesting possible biomarkers for patient stratification by resistance profiles. Overall, these findings provide new avenues for developing personalized treatment strategies for GBM and can contribute to improving the prognosis of GBM patients.