Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

Modrek, A. S.; Chandradoss, K. R.; Do, C.; Ezhilarasan, R.; Sakellaropoulos, T.; Karp, J.; Ding, Y.; Zhang, Z.-Y.; Graciani, M.; Cova, G.; Phillips-Cremins, J. E.; Sulman, E. P.; Skok, J. A.

doi:10.1101/2025.06.18.660431

bioRxiv · 10.1101/2025.06.18.660431

Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

Modrek, A. S.·Chandradoss, K. R.·Do, C.·Ezhilarasan, R.·Sakellaropoulos, T.·Karp, J.·Ding, Y.·Zhang, Z.-Y.·Graciani, M.·Cova, G.·Phillips-Cremins, J. E.·Sulman, E. P.·Skok, J. A.

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Abstract

DNA damage from routine cellular processes or exogenous insults can have a lasting impact on gene regulation beyond genetic mutations. The prevailing paradigm for the consequences of DNA damage repair revolves around restoration of the original genetic sequence, but long-term changes in chromatin configuration, gene expression and DNA modifications have not been analyzed. We introduced numerous, simultaneous Cas9-mediated DNA double strand breaks (DSBs) at defined locations in human glioblastoma cells and tracked both non-genetic and genetic alterations over time. Megabase-scale genomic alterations that endured two weeks after the initial damage were detected, involving a shift from transiently increased intra-TAD interactions to persistent long range cis and trans contacts, alterations in gene-expression and associated large structural variations. These findings reveal that widespread DNA damage, such as chemotherapy or radiotherapy, can trigger long-term genetic and non-genetic modifications which alter cellular function and may impact tumor outcome and the emergence of resistant cells.

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Modrek, A. S., Chandradoss, K. R., Do, C., Ezhilarasan, R., Sakellaropoulos, T., Karp, J., Ding, Y., Zhang, Z.-Y., Graciani, M., Cova, G., Phillips-Cremins, J. E., Sulman, E. P., Skok, J. A.. 2025-06-24. Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma. https://doi.org/10.1101/2025.06.18.660431

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