Leveraging chromatin packing domains to target chemoevasion in vivo

Frederick, J.; Virk, R. K. A.; Ye, I. C.; Almassalha, L. M.; Wodarcyk, G. M.; VanDerway, D.; Carrillo Gonzalez, P.; Nap, R. J.; Agrawal, V.; Anthony, N. M.; Carinato, J.; Li, W. S.; Dunton, C. L.; Medina, K. I.; Kakkaramadam, R.; Jain, S.; Shahabi, S.; Ameer, G.; Szleifer, I. G.; Backman, V.

doi:10.1101/2024.11.14.623612

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bioRxiv · 10.1101/2024.11.14.623612

Leveraging chromatin packing domains to target chemoevasion in vivo

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Abstract

Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains (TADs). However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based mechanistic model that connects chromatin organization to cell fate decisions, specifically survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional efficiency through macromolecular crowding. The model accurately predicts chemoevasion in vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. Using live-cell chromatin imaging, we conducted a compound screen that identified several TPRs which synergistically enhanced chemotherapyinduced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft (PDX) model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a novel framework for enhancing cancer therapies, with broad potential across multiple cancer types.

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Frederick, J., Virk, R. K. A., Ye, I. C., Almassalha, L. M., Wodarcyk, G. M., VanDerway, D., Carrillo Gonzalez, P., Nap, R. J., Agrawal, V., Anthony, N. M., Carinato, J., Li, W. S., Dunton, C. L., Medina, K. I., Kakkaramadam, R., Jain, S., Shahabi, S., Ameer, G., Szleifer, I. G., Backman, V.. 2024-11-15. Leveraging chromatin packing domains to target chemoevasion in vivo. https://doi.org/10.1101/2024.11.14.623612

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