PUM3 is an essential suppressor of replication stress in homologous recombination deficient breast cancer

Most Triple Negative Breast Cancers (TNBCs) are p53 mutant high-grade invasive ductal carcinomas with a basal-like transcriptional programme. A large proportion of TNBCs also have mutation signatures indicating defective homologous recombination (HR) DNA repair. While HR deficiency is mutagenic and oncogenic, it can also compromise cell fitness. Here, we show that BLBCs harbouring the recurrent 9p21.3–9p24 amplicon, and particularly those that are HR-defective, overexpress PUM3 (Pumilio RNA binding family member 3). PUM3 inhibition is also synthetic lethal in tumour cells that overexpress PUM3 including those that have BRCA1/BRCA2 defects. Mechanistically, PUM3 suppresses transcription-mediated replicative stress and R-loop accumulation, thereby preventing DNA damage that would normally require RAD51-mediated repair. Transcription/replication collisions are commonly resolved by topoisomerase TOP1; without PUM3, TOP1 DNA chromatin localisation is impaired, revealing one mechanism by which PUM3 limits replication stress. PUM3 is therefore required for the continued fitness of a BLBC subset, allowing tolerance of HR deficiency’s deleterious effects. How tumour cells survive defective homologous recombination (HR) DNA repair has not been fully understood. Here the authors find that PUM3 prevents transcription replication conflicts and accumulation of R-loops through recruiting the DNA topoisomerase TOP1 in HR-defective triple negative breast cancer cells.