Cyclin E modulates vulnerability to CDC7 kinase inhibition

CCNE1 (cyclin E) is frequently amplified or overexpressed in triple-negative breast cancer (TNBC) as compared with luminal subtypes. Cyclin E is associated with chromosomal instability and poor outcome, and overexpression promotes replication stress (fork stalling) in S-phase through impaired MCM chromatin loading and deregulated replication origin firing. Thus, approaches leveraging cyclin E-induced replication stress could lead to the development of promising therapeutic strategies. Here, we studied the effects of cell division cycle 7 (CDC7) kinase inhibition in TNBC cells overexpressing cyclin E. Cyclin E overexpression enhanced sensitivity to CDC7 inhibition, reducing proliferation and colony-forming capacity. This was accompanied by delays in replication timing and cell accumulation with ≥4 N DNA content. Conversely, CCNE1 knockdown rescued proliferation and colony outgrowth in the presence of CDC7 inhibition and reversed accumulation with ≥ 4N DNA content. CRISPR screening revealed cyclin-dependent kinase 8 (CDK8) as conferring resistance to CDC7 inhibition in a CCNE1-amplified cell line. Combined CDC7 and CDK8 inhibition significantly reduced proliferation and colony-forming ability, led to ≥4 N DNA content, and reduced tumor volume and mass in vivo. Together, this work identifies the enhanced vulnerability of cyclin E-overexpressing TNBC cells to CDC7 kinase inhibition and substantial synergy when combined with CDK8 inhibition.