Identification and characterisation of drug-tolerant persister cells arising in response to targeted CHK1 inhibition

Abstract

Drug-tolerant persisters (DTPs) are a subpopulation of slow-cycling cells that have been identified in several cancer cell lines following lethal exposure to targeted and cytotoxic therapeutics and shown to precede acquisition of diverse and clinically relevant drug resistance mechanisms. To date, much of the data comes from studies using tyrosine kinase inhibitors and it is unclear if this persister phenotype is broadly observed in response to drugs that act by various anti-tumour mechanisms. Herein, a subpopulation of slow-cycling SK-N-AS cells survived treatment with lethal concentrations of SRA737; a clinically relevant CHK1 inhibitor. Surviving cells represent a large proportion of the starting population and have increased global histone H3 lysine 27 trimethylation (H3K27me3). Continued lethal SRA737 exposure leads to the emergence of a drugtolerant expanded persister (DTEP) population, marked by resumed proliferation and cross-resistance to other small molecule CHK1/CHK2 and DNA damage response (DDR) inhibitors. H3K27me3 remains elevated in DTEPs but is diminished after drug release, suggesting a role for epigenetic regulation/reprogramming in both DTP formation and progression. Inhibition of the H3K27 methyltransferase EZH2 using tazemetostat inhibits DTP-to-DTEP transition but fails to abrogate DTP formation or DTEP survival, confirming the requirement of epigenetic plasticity for persister cell progression. Comparison to SRA737 resistant populations generated by dose-escalation revealed differential responses to further CHK1 inhibition and specific enrichment of genes associated with JAK-STAT signalling in persister-derived populations. Interestingly, exogenous IFNγ, but not JAK inhibition, delayed the emergence of a drug resistant population from an SRA737-induced DTP bottleneck, suggesting that overactivation of the IFNγ signalling pathway is detrimental to DTP progression. In conclusion, I have characterised DTPs arising within a novel and clinically relevant therapeutic context, defined differences between pathways to drug resistance through DTPs and dose escalation, and uncovered EZH2 activity and IFNγ signalling as potential intervention points to eradicate this persistent population.