# Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance

## TL;DR

The study shows that variable expression of the FOXM1 gene helps cancer cells survive DNA-damaging drugs, offering new insights into drug resistance.

## Contribution

The study reveals that partial suppression of FOXM1 and its targets can protect cells from DNA damage during replication stress.

## Key findings

- 37 genes, including FOXM1 targets, are differentially expressed in drug-tolerant versus sensitive cells.
- Partial FOXM1 knockdown reduces DNA damage and improves recovery from replication stress.
- UBE2C and MKI67, FOXM1 targets, play unexpected roles in the replication stress response.

## Abstract

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 intra‐S‐phase checkpoint kinases ATR and CHK1 have been developed, but resistance to these drugs remains 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 single‐cell RNA‐sequencing, we characterized the transcriptomes of oncogenic RAS‐expressing cells with variable levels of RS when challenged with a CHK1 inhibitor combined with gemcitabine. We identified 37 genes differentially expressed between tolerant and sensitive cells, including several FOXM1 targets. While complete knockdown of FOXM1 impeded cell proliferation, partial knockdown protected cells against DNA damage, and improved recovery from drug‐induced RS. Remarkably, knockdown of individual FOXM1 target genes UBE2C and MKI67 also mitigated DNA damage, uncovering unanticipated roles for these in the replication stress response. Our results suggest that low levels of FOXM1‐dependent gene expression during S and G2 phase protects cells against excessive DNA damage during drug‐induced replication stress.

Cellular heterogeneity is a major cause of drug resistance in cancer. Segeren et al. used single‐cell transcriptomics to investigate gene expression events that correlate with sensitivity to the DNA‐damaging drugs gemcitabine and prexasertib. They show that dampened expression of transcription factor FOXM1 and its target genes protected cells against excessive DNA damage during S‐ and G2‐phases of the cell cycle.