HMCES corrupts replication fork stability during base excision repair in homologous recombination–deficient cells

Apurinic/apyrimidinic (AP) sites and single-strand breaks arising from base excision repair (BER) during the misincorporation of damaged nucleobases may hinder replication fork stability in homologous recombination–deficient (HRD) cells. At templated AP sites, cross-links between the DNA and 5-hydroxymethylcytosine binding, embryonic stem cell–specific (HMCES) regulate replication fork speed, avoiding cytotoxic double-strand breaks. While the role of HMCES at the template DNA strand is well studied, its effects on nascent DNA are not. We provide evidence that HMCES–DNA-protein cross-links (DPCs) are detrimental to the BER-mediated removal of 5-hydroxymethyl-2′-deoxycytidine (5hmdC)–derived 5-hydroxymethyl-2′-deoxyuridine from replication forks. HRD cells have heightened HMCES-DPCs, which increase further upon 5hmdC exposure, suggesting that HMCES binds both spontaneous and 5hmdC-induced AP sites. HMCES depletion substantially suppresses 5hmdC-mediated replication fork defects, chromosomal aberrations, and cell death in HRD cells. This reveals that HMCES-DPCs are a source of BER-initiated single-stranded DNA gaps, which indicates that endogenous DPCs contribute to genomic instability in HRD tumors.