Abstract 1167: Targeting DNA repair pathways in PDAC: APE1 BER and its therapeutic role in PDAC homeostasis
Authors: Eyram K. Kpenu, Silpa Gamapala, Mahmut Mijit, Randall Wireman, Melissa Fishel, Mark R. Kelley
Journal: Cancer Research (2025)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest malignancies due to its resistance to therapeutic strategies and ability to thrive under extreme tumor microenvironment conditions. The cancer's ability to adaptively resist treatments underscores the need for novel and combinatorial therapeutic approaches. Apurinic-apyrimidinic endonuclease/Redox effector factor 1 (APE1/Ref-1) is a critical protein in PDAC pathobiology. APE1 serves two essential functions: as the principal endonuclease in the base excision repair (BER) pathway for DNA repair and as a redox regulator of transcription factors essential for cancer cell proliferation. Targeting APE1’s redox function has already demonstrated therapeutic potential. The development of treatments aimed at its BER function, however, has proven more challenging, with limited progress to date. Since standard PDAC treatment regimens involve DNA damaging agents potentially repaired via BER and APE1, we engineered cell lines with knock-in mutations resulting in a reduction of APE1’s BER activity while maintaining full redox signaling activity. Biochemical evaluations confirmed a 30-fold reduction in DNA repair capacity. Despite this impairment, the mutant and wild-type cell lines exhibited similar sensitivity to cytotoxic DNA damaging agents in short-term proliferation assays. We posited that the mutant cell lines were relying on compensatory DNA repair pathways which could provide sufficient compensation for the decrease in APE1 activity. We further hypothesized that the cell lines had hidden, long-term deficiencies in DNA damage processing not apparent during the initial stress response. Subsequent long-term functional assays revealed significant vulnerabilities in the mutant cell lines. Colony formation assays revealed that the mutant cell lines exhibit poor long-term survival after short-term exposure to DNA damage. These findings were recapitulated in vivo with orthotopic mouse models which demonstrated significant reductions in tumor size and decreased metastasis to the lungs and liver in mutant cell lines compared to wild-type controls. These findings suggest that, while compensatory DNA repair pathways support short-term survival, they may be insufficient to manage DNA damage long-term, resulting in delayed but substantial deficiencies in tumor cell survival. While APE1 is the primary endonuclease in the BER pathway, studies have demonstrated APE1-independent BER in rare contexts. We hypothesize that these APE1-independent BER pathways may function as the compensatory mechanism safeguarding these cells in short-term stress conditions. Characterizing these compensatory pathways will offer a better understanding of how APE1’s BER mechanisms contribute to PDAC homeostasis and how these mechanisms can be therapeutically targeted. This work opens the path to enhance standard of care treatments such as FOLFIRINOX. Citation Format: Eyram K. Kpenu, Silpa Gamapala, Mahmut Mijit, Randall Wireman, Melissa Fishel, Mark R. Kelley. Targeting DNA repair pathways in PDAC: APE1 BER and its therapeutic role in PDAC homeostasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1167.