Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

Chowdhury, T.; Tesileanu, C. M. S.; Kocakavuk, E.; Johnson, K. C.; Lee, J.; Erson-Omay, Z.; Heo, C.; Aldape, K.; Amin, S. B.; Anderson, K. J.; Ashley, D. M.; Barnholtz-Sloan, J. S.; Brat, D. J.; Brodbelt, A. R.; Castro, A. V.; Claus, E. B.; Connelly, J. M.; Costello, J.; Datta, I.; Elliott, C.; Finocchiaro, G.; French, P. J.; Gan, H. K.; Garofano, L.; Ghospurkar, P. L.; Golebiewska, A.; Gundla, P. S.; Hermes, B.; Hong, C.; Hoogstrate, Y.; Horbinski, C.; Huse, J. T.; Iavarone, A.; Karadag, C.; Khasraw, M.; Kouwenhoven, M. C.; LaViolette, P. S.; Li, K.; Lowman, A.; McCortney, K.; Moon, H.-E.; Na

doi:10.1101/2025.07.11.664189

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bioRxiv · 10.1101/2025.07.11.664189

Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

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Abstract

Astrocytomas and oligodendrogliomas are slow-growing and treatment-sensitive IDH-mutant gliomas diagnosed at ages 30-50. Local tumor regrowth and treatment resistance is inevitable resulting in 3-10 year astrocytoma and up to >20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy.

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Chowdhury, T., Tesileanu, C. M. S., Kocakavuk, E., Johnson, K. C., Lee, J., Erson-Omay, Z., Heo, C., Aldape, K., Amin, S. B., Anderson, K. J., Ashley, D. M., Barnholtz-Sloan, J. S., Brat, D. J., Brodbelt, A. R., Castro, A. V., Claus, E. B., Connelly, J. M., Costello, J., Datta, I., Elliott, C., Finocchiaro, G., French, P. J., Gan, H. K., Garofano, L., Ghospurkar, P. L., Golebiewska, A., Gundla, P. S., Hermes, B., Hong, C., Hoogstrate, Y., Horbinski, C., Huse, J. T., Iavarone, A., Karadag, C., Khasraw, M., Kouwenhoven, M. C., LaViolette, P. S., Li, K., Lowman, A., McCortney, K., Moon, H.-E., Na. 2025-07-15. Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas. https://doi.org/10.1101/2025.07.11.664189

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