Stochastic variation in the FOXM1 transcription program mediates replication stress tolerance

Area of Science:

• Molecular Biology
• Cancer Biology
• Genomics

Background:

• Oncogene-induced replication stress (RS) is a key cancer vulnerability.
• Intra-S-phase checkpoint inhibitors (e.g., ATR, CHK1) face drug resistance.
• Bulk sample analysis hinders understanding of tumor heterogeneity and resistance mechanisms.

Purpose of the Study:

• To characterize transcriptomes of cancer cells under replication stress (RS) and CHK1 inhibition.
• To identify mechanisms of drug tolerance in oncogenic RAS-expressing cells.
• To investigate the role of FOXM1 and its targets in drug resistance.

Main Methods:

• Intracellular immunostaining combined with single-cell RNA-sequencing.
• Analysis of oncogenic RAS-expressing cells under CHK1 inhibitor and gemcitabine treatment.
• Gene knockdown experiments (FOXM1, UBE2C, MKI67).

Main Results:

• Identified 37 differentially expressed genes between drug-tolerant and sensitive cells, including FOXM1 targets.
• Partial FOXM1 knockdown protected cells from DNA damage and improved recovery from drug-induced RS.
• Knockdown of FOXM1 target genes UBE2C and MKI67 also mitigated DNA damage.

Conclusions:

• Low levels of FOXM1-dependent gene expression during S and G2 phases protect against excessive DNA damage during drug-induced RS.
• FOXM1 and its target genes (UBE2C, MKI67) play critical roles in the replication stress response.
• Findings suggest novel therapeutic strategies targeting FOXM1 in cancer treatment.