Targeting chromatin mediated cellular plasticity in vivo

Advances in cancer treatment, including precision oncology, are significantly hindered by cancer cell plasticity. The ability to adapt to various external stressors is due to two attributes of highly plastic cells: transcriptional malleability, which is the ability of a cell to quickly upregulate survival pathways, and transcriptional heterogeneity, or the variance in the pathways utilized by cells to evade cell death. Both aspects of phenotypic plasticity have been directly linked to a measure of statistical chromatin organization, the chromatin packing scaling D, which facilitates changes in gene expression. To study the role of chromatin in plasticity-mediated survival, we performed time-course imaging of chemotherapy-treated cancer cells using label-free Partial Wave Spectroscopic (PWS) microscopy. The population distribution of D shifted over the course of treatment such that all surviving cells exhibited high D values. Accordingly, cell cluster tracking demonstrated a negative correlation between the initial D and the increase in D induced by treatment. We developed a computational model of cell fate based on changes in transcription due to D, which could recapitulate experimental results. We predicted that pharmacologically lowering D would reduce plasticity and improve chemotherapeutic efficacy. Specifically, we screened compounds that would lower D by facilitating chromatin-nucleoplasm interactions through either histone tail modifications or changes in the nuclear ionic environment. Adding a D-lowering agent to chemotherapy treatment increased the probability of cell death compared to chemotherapy alone, which matched model predictions. We next tested these treatments in vivo in a PDX model where our model predicted that although tumors would still be able to adapt to chemotherapy treatment, the combination treatment would exhibit a higher cell growth inhibition rate and stunt tumor adaptation. Significantly, our results demonstrated that lowering D improves treatment outcomes even in a conservative treatment with low-dose chemotherapy.