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Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets
Kristen E Mengwasser1, Richard O Adeyemi1, Yumei Leng1
1Howard Hughes Medical Institute, Department of Genetics, Ludwig Center, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
Abstract:
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.
Insights
BRCA1/BRCA2-deficient cancers show synthetic lethality with inhibition of APEX2 and FEN1. Targeting these DNA repair pathways offers new therapeutic strategies for breast and ovarian cancers.
Area of Science:
- Genetics
- Molecular Biology
- Cancer Research
Background:
- BRCA1 or BRCA2 gene inactivation is a key driver of breast and ovarian cancers.
- This inactivation confers sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors.
- Identifying additional synthetic lethal targets in BRCA-deficient cancers is crucial for developing novel therapies.
Purpose of the Study:
- To identify novel genes and pathways that are synthetically lethal with BRCA2 loss of function.
- To explore potential therapeutic targets for BRCA1/BRCA2-deficient cancers.
Main Methods:
- Screening of BRCA2 isogenic cell lines using small hairpin RNA (shRNA) and CRISPR-based libraries.
- Functional characterization of identified synthetic lethal genes, including APEX2 and FEN1.
- Development of a microhomology-mediated end-joining (MMEJ) reporter assay.
Main Results:
- BRCA2-deficient cells exhibit selective dependency on base excision repair, ATR signaling, and splicing pathways.
- APEX2 and FEN1 were identified as synthetic lethal genes upon BRCA1/BRCA2 loss.
- FEN1 inhibition selectively targets BRCA-deficient cells, and FEN1 participates in MMEJ.
Conclusions:
- APEX2 and FEN1 are critical for the survival of BRCA-deficient cells.
- Targeting APEX2 or FEN1 represents a promising synthetic lethal strategy for BRCA-mutated cancers.
- MMEJ is an important collateral DNA repair pathway in homologous recombination-deficient contexts.
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