CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition

Abstract

Amplification of the CCNE1 locus on chromosome 19q12 is prevalent in multiple tumour types, particularly in high-grade serous ovarian cancer, uterine tumours and gastro-oesophageal cancers, where high cyclin E levels are associated with genome instability, whole-genome doubling and resistance to cytotoxic and targeted therapies1–4. To uncover therapeutic targets for tumours with CCNE1 amplification, we undertook genome-scale CRISPR–Cas9-based synthetic lethality screens in cellular models of CCNE1 amplification. Here we report that increasing CCNE1 dosage engenders a vulnerability to the inhibition of the PKMYT1 kinase, a negative regulator of CDK1. To inhibit PKMYT1, we developed RP-6306, an orally bioavailable and selective inhibitor that shows single-agent activity and durable tumour regressions when combined with gemcitabine in models of CCNE1 amplification. RP-6306 treatment causes unscheduled activation of CDK1 selectively in CCNE1-overexpressing cells, promoting early mitosis in cells undergoing DNA synthesis. CCNE1 overexpression disrupts CDK1 homeostasis at least in part through an early activation of the MMB–FOXM1 mitotic transcriptional program. We conclude that PKMYT1 inhibition is a promising therapeutic strategy for CCNE1-amplified cancers.

The spindle assembly checkpoint is a therapeutic vulnerability of CDK4/6 inhibitor–resistant ER + breast cancer with mitotic aberrations

“…For instance, RB1 loss, which causes chromosome segregation errors, micronuclei, and DNA damage in different tumor models, induces sensitivity to targeted inhibitors of the mitotic regulators polo-like kinase 1 (PLK1) and Aurora kinase A/B ( 20 , 22 , 26 – 29 ). Moreover, Gallo et al ( 30 ) have demonstrated that CCNE1 overexpression, which can override the G 1 -S checkpoint and cause resistance to CDK4/6i, sensitizes cancer cells to PKMYT1 inhibition, causing cell death through premature entry into mitosis and mitotic catastrophe. A recent study by Crozier et al ( 31 ) demonstrated that short-term CDK4/6i treatment induced replication stress and genomic instability in immortalized RPE1 cells.…”

Discovery of an Orally Bioavailable and Selective PKMYT1 Inhibitor, RP-6306

“…The synthetic lethal relationship between CCNE1 amplification and the absence of PKMYT1 activity was confirmed both genetically and chemically (with RP-6306 ) through comparison of the growth sensitivity of isogenic fallopian tube cells (FT282 cells) engineered to overexpress CCNE1 relative to wild-type cells . Furthermore, multiple cancer cell lines and xenograft models with amplified CCNE1 or cyclin E over-expression showed greater growth inhibition compared to normal counterparts . Using a very sensitive and robust CCNE1 -amplified ovarian xenograft model (OVCAR3), we sought to understand the relationship between target inhibition, RP-6306 exposure, and efficacy.…”

“…PKMYT1 function does not appear to be critical in the unperturbed cell cycle, whereas WEE1 function is essential for cell cycle progression of cells . However, the absence of functional PKMYT1 in a genetically vulnerable tumor, such as with CCNE1 amplification, causes cells to lose major checkpoint regulation leading to hyperactive CDK1, unscheduled mitosis and catastrophic DNA damage, ultimately resulting in cell death . No selective inhibitors have been previously reported for PKMYT1 that would allow for the investigation of the pharmacological activity.…”

Comprehensive Analysis of Genomic Alterations in Hepatoid Adenocarcinoma of the Stomach and Identification of Clinically Actionable Alterations

“…For example, chr8q24.21 amplification was frequent in advanced GC [ 31 ], and involved in liver metastasis of rectal adenocarcinoma [ 32 ]. chr19q12 amplification was prevalent in multiple tumor types [ 33 ]. Consistently, in 65.8% of HAS cases there existed the amplification of chr19q12.…”

“…Consistently, in 65.8% of HAS cases there existed the amplification of chr19q12. Amplification of the CCNE1 locus in this region was synthetic lethal related, targeted by PKMYT1 kinase inhibition, and it was also a promising target in AFPGC, which warranted further research in HAS [ 10 , 33 ]. Deleted regions-associated studies were mainly involved in gastrointestinal defects, Peutz-Jeghers syndrome (19p13.3), and immunodeficiency (14q32.33) [ 34 , 35 , 36 , 37 ].…”