Supporting data for Molecular mechanisms of PARP inhibitor sensitivity in FANCM-Deficient cells

PARP inhibitors (PARPis) display significant anticancer activity in tumors carrying mutations in BRCA1/BRCA2 or other genes required for homologous recombination (HR). However, how other DNA repair proteins are involved in PARPi-induced lethality remains unclear. Here, we show that FANCM-depleted cells, but not FANCB-depleted cells, are hypersensitive to PARPi, indicating that FANCM promotes PARPi resistance independent of the core FA complex. FANCM-depleted cells are HR-proficient and FANCM acts independently of BRCA1 in response to PARPi. Importantly, we show that FANCM-depleted cells display an elevated level of DNA damage in the second S phase after PARPi exposure due to an increased formation of ssDNA gaps behind replication forks in the first S phase. Strikingly, FANCM-depleted cells also exhibit reduced DNA resection of collapsed forks in the second S phase, resulting in chromosome fusion and chromatin bridges in the following mitosis. Our results lead us to propose a model in which FANCM plays a dual role in repairing PARPi-induced lesions. PARP1 trapping induced by PARPi inhibits the processing of unligated Okazaki fragments. FANCM prevents the formation of ssDNA gaps by counteracting 53BP1, which has been shown to inhibit Okazaki fragment processing. In the second S phase, collisions of the replication forks with ssDNA gaps lead to fork collapse and one-ended DSBs. Another role of FANCM is to facilitate the repair of the collapsed forks via HR as it promotes the resection of DSBs at collapsed forks by counteracting 53BP1, an inhibitor of resection. In the absence of FANCM, resection is inhibited by 53BP1, and error-prone repair via NHEJ will be promoted to repair the collapse forks, leading to structural chromosomal instability such as radial chromosomes and chromatin bridges. This project provides the potential to extend the license for use beyond BRAC-deficient tumors, expand indications beyond breast and ovarian cancers, and enhance the efficacy of PARPi combination therapy.