Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance

Oncogene-induced replication stress (RS) is a vulnerability of cancer cells that forces reliance on the intra-S-phase checkpoint to ensure faithful genome duplication. Inhibitors of the crucial intra-S-phase checkpoint kinases ATR and CHK1 have been developed, but persistent proliferation and resistance to these drugs remain problematic. Understanding drug tolerance mechanisms is impeded by analysis of bulk samples, which neglect tumor heterogeneity and often fail to accurately interpret cell cycle-mediated resistance. Here, by combining intracellular immunostaining and RNA-sequencing of single cells, we characterized the transcriptomes of oncogenic RAS-expressing cells that exhibit variable levels of RS when challenged with a CHK1 inhibitor in combination with the chemotherapeutic drug gemcitabine. We identified 40 genes differentially expressed between tolerant and sensitive cells, including several FOXM1 target genes. While complete knockdown of FOXM1 impeded cell proliferation, a partial knockdown protected cells against DNA damage, and improved recovery from drug-induced RS. Our results suggest that low levels of FOXM1 expression protects subsets of oncogenic RAS-expressing cells against DNA damage during drug-induced replication stress.