Schlafen 11 (SLFN11) kills cancer cells undergoing unscheduled re-replication.

SLFN11 is an increasingly prominent predictive biomarker and a molecular sensor for a wide range of clinical drugs: topoisomerases, PARP and replication inhibitors, and platinum derivatives. To expand the spectrum of drugs and pathways targeting SLFN11, we ran a high-throughput screen (HTS) with 1,978 mechanistically-annotated, oncology-focused compounds in two isogenic pairs of SLFN11-proficient and -deficient cells (CCRF-CEM and K562). We identified 29 hit compounds that selectively kill SLFN11-proficient cells, including not only previously known DNA-targeting agents, but also the neddylation inhibitor Pevonedistat (MLN-4924) and the DNA polymerase alpha inhibitor AHPN/CD437, which both induced SLFN11 chromatin recruitment. By inactivating cullin-ring E3 ligases, Pevonedistat acts as an anticancer agent partly by inducing unscheduled re-replication through supra-physiological accumulation of CDT1, an essential factor for replication initiation. Unlike the known DNA-targeting agents and AHPN/CD437 that recruit SLFN11 onto chromatin in 4 hours, Pevonedistat recruited SLFN11 at late time points (24 hours). While Pevonedistat induced unscheduled re-replication in SLFN11-deficient cells after 24 hours, the re-replication was largely blocked in SLFN11-proficient cells. The positive correlation between sensitivity to Pevonedistat and SLFN11 expression was also observed in non-isogenic cancer cells in three independent cancer cell databases (NCI-60, CTRP: Cancer Therapeutics Response Portal and GDSC: Genomic of Drug Sensitivity in Cancer). The present study reveals that, in addition to sensing stressed replication, SLFN11 blocks unscheduled re-replication provoked by Pevonedistat, which augments the anti-cancer effect of Pevonedistat. It also suggests SLFN11 as a potential predictive biomarker for Pevonedistat in ongoing and future clinical trials.