Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets

BRCA1 or BRCA2 inactivation drives breast and ovarian cancer but also creates vulnerability to poly(ADP-ribose) polymerase (PARP) inhibitors. To search for additional targets whose inhibition is synthetically lethal in BRCA2-deficient backgrounds, we screened two pairs of BRCA2 isogenic cell lines with DNA-repair-focused small hairpin RNA (shRNA) and CRISPR (clustered regularly interspaced short palindromic repeats)-based libraries. We found that BRCA2-deficient cells are selectively dependent on multiple pathways including base excision repair, ATR signaling, and splicing. We identified APEX2 and FEN1 as synthetic lethal genes with both BRCA1 and BRCA2 loss of function. BRCA2-deficient cells require the apurinic endonuclease activity and the PCNA-binding domain of Ape2 (APEX2), but not Ape1 (APEX1). Furthermore, BRCA2-deficient cells require the 5′ flap endonuclease but not the 5′-3′ exonuclease activity of Fen1, and chemically inhibiting Fen1 selectively targets BRCA-deficient cells. Finally, we developed a microhomology-mediated end-joining (MMEJ) reporter and showed that Fen1 participates in MMEJ, underscoring the importance of MMEJ as a collateral repair pathway in the context of homologous recombination (HR) deficiency. [Display omitted] •BRCA2-mutant cells rely on BER, ATR signaling, splicing, and MMEJ for survival•APEX2 and FEN1 represent potential drug targets in BRCA-mutant tumors•BRCA-mutant cells require the endonuclease function and PCNA association of APEX2•A cell-based reporter demonstrates that FEN1 participates in MMEJ Mengwasser et al. perform several genetic screens to systematically identify genes and pathways required for BRCA2-mutant cell survival. They find that BRCA2-mutant cells rely on base excision repair, ATR signaling, splicing, and MMEJ. APEX2 and FEN1, involved in replication-associated BER and MMEJ, respectively, are potential targets in BRCA-mutant tumors.