FANCM restrains structural genome evolution and defines a synthetic lethal dependency in BRCA1 -deficient breast cancer

BRCA1 -deficient cancers experience persistent replication stress and structural genome instability yet retain the capacity for sustained proliferation, implying reliance on compensatory genome-maintenance mechanisms. Here, we establish BRCA1–FANCM synthetic lethality in human BRCA1 -deficient breast cancer and exploit temporally controlled FANCM depletion to capture genome evolution over successive cell divisions before declining cellular fitness becomes limiting. We show that FANCM restrains genome-wide structural variation in BRCA1 -deficient breast cancer cells under endogenous replication stress. FANCM loss amplifies the characteristic BRCA1 -associated short tandem duplication (TD) phenotype while permitting larger, including megabase-scale, TDs and diverse rearrangements to emerge. Newly emerged TDs preferentially associate with Pol II-occupied regions, and FANCM depletion increases proximity between the replication machinery and elongating RNAPII in BRCA1 -mutant breast cancer cells, linking FANCM-mediated genome protection to transcription–replication encounters. BRCA1 -altered human tumors with low FANCM expression recapitulate key features of this phenotype, while genome–transcriptome integration links newly emerged SVs to configuration-dependent local transcriptional changes. Together, these findings establish FANCM as a replication-stress safeguard coupling survival to restraint of structural genome evolution.