Genetic screening for single-cell variability modulators driving therapy resistance

Torre, E. A.; Arai, E.; Bayatpour, S.; Beck, L. E.; Emert, B. L.; Shaffer, S. M.; Mellis, I. A.; Budinich, K. A.; Weeraratna, A.; Shi, J.; Raj, A.

doi:10.1101/638809

bioRxiv · 10.1101/638809

Genetic screening for single-cell variability modulators driving therapy resistance

Torre, E. A.·Arai, E.·Bayatpour, S.·Beck, L. E.·Emert, B. L.·Shaffer, S. M.·Mellis, I. A.·Budinich, K. A.·Weeraratna, A.·Shi, J.·Raj, A.

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Abstract

Cellular plasticity describes the ability of cells to transition from one set of phenotypes to another. In the context of cancer therapeutics, plasticity refers to transient fluctuations in the molecular state of tumor cells, driving the formation of rare cells primed to survive drug treatment and ultimately reprogram into a stably resistant fate. However, the biological processes governing this cellular plasticity remain unknown. We used CRISPR/Cas9 genetic screens to reveal genes that affect cell fate decisions by altering cellular plasticity across a range of functional categories. We found that cellular plasticity and cell fate decision making can be decoupled in that factors can affect cell fate decisions in both plasticity-dependent and independent manners. We discovered a novel mode of altering resistance based on cellular plasticity that, contrary to known mechanisms, pushes cells towards a more differentiated state. We further confirmed our prediction that manipulating cellular plasticity before the addition of the main therapy would result in changes in therapy resistance more than concurrent administration. Together, our results indicate that identifying pathways modulating cellular plasticity has the potential to alter cell fate decisions and may provide a new avenue for treating drug resistance.

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Torre, E. A., Arai, E., Bayatpour, S., Beck, L. E., Emert, B. L., Shaffer, S. M., Mellis, I. A., Budinich, K. A., Weeraratna, A., Shi, J., Raj, A.. 2019-05-15. Genetic screening for single-cell variability modulators driving therapy resistance. https://doi.org/10.1101/638809

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