Positional replication fork instability drives PARP inhibitor cytotoxicity

Although poly(ADP-ribose) polymerase inhibitors (PARPi) show promise for treating homologous recombination-deficient cancers, the observed PARPi hypersensitivity in additional genetic contexts expands their potential use in precision oncology. Yet, the DNA lesions driving PARPi-induced cytotoxicity remain poorly defined. Here we uncover distinct replication-fork lesions in specific genomic regions as key determinants of PARPi cytotoxicity. Using CRISPR screens, we identify that loss of replication-coupled cohesin acetyltransferase ESCO2 confers PARPi hypersensitivity independently of homologous recombination deficiency. Quantitative single-molecule imaging reveals that ESCO2 loss promotes accumulation of G-quadruplex (G4) DNA structures at a subset of replication-associated sites, associated with PARP1 activation and engagement of fork protection factor TIMELESS to mitigate G4-induced stress. Notably, these G4 lesions localize to fragile pericentromeric regions and engage the G4 helicase DDX11. PARP inhibition disrupts this protective G4-processing response by preventing PARP1-dependent engagement of TIMELESS and DDX11, leading to G4 accumulation, DNA damage and chromosomal instability. Together, our findings define the G4-PARP1-TIMELESS-DDX11 axis as a critical safeguard of replication fork stability at hard-to-replicate loci and reveal ESCO2 as a therapeutic target for promoting synthetic lethality in PARPi-treated cancers.