Investigating the Role of Mutagenic DNA Repair during the Persistence of Cancer Cells

PROJECT SUMMARY/ABSTRACT Our cells possess multiple mechanisms for repairing DNA to safeguard our genomes. While predominantly error-free pathways such as homologous recombination (HR) are responsible for maintaining genomic integrity, low-fidelity repair mechanisms such as non-homologous end joining (NHEJ) contribute to genomic plasticity. When cells are under extreme stress, such as being exposed to anti-cancer drugs, they enter a state of persistence where low-fidelity DNA polymerases are upregulated and HR is downregulated, shifting dependence of DNA repair to error-prone mechanisms. If mutations occur in genes targeted by the anti-cancer drug, they can result in acquired drug resistance and lead to cancer relapse. In BRCA1/2-mutant cancers, which are HR-deficient, initial tumor response to DNA-damaging poly-ADP ribose polymerase (PARP) inhibitors is mitigated by reversion mutations that restore BRCA1/2 function and therefore HR. These resistance-conferring reversion mutations are often flanked by regions of microhomology, suggesting the involvement of the mutagenic DNA repair pathway, microhomology-mediated end joining (MMEJ). In colorectal cancer (CRC), initial tumor response to epidermal growth factor receptor (EGFR) blockade is mitigated by acquired resistance-conferring point mutations in EGFR, KRAS, and other genes. As such, understanding persistence and mutagenic DNA repair is critical for studying and treating cancer. However, the specific mechanisms that promote mutagenic DNA repair and drive acquired drug resistance in persister cancer cells remain unclear. We hypothesize that cellular stress induced by anti-cancer drugs rewires DNA repair pathways in persister cancer cells, increases their reliance on mutagenic DNA repair—by MMEJ—and drives the emergence of acquired resistance mutations. This proposal describes work to define the role of MMEJ in persistence-mediated acquired resistance in cancer cells by (1) investigating persistence in response to PARPi treatment of BRCA1/2 cancer cells; (2) examining mechanisms of mutagenic DNA repair in persister colorectal cancer cells; and (3) using high-content microscopy to determine a morphological signature of persistence. Given the clinical importance of persistence in cancer, this work has the potential to directly impact cancer treatment by identifying potential therapeutic targets, particularly regulators of MMEJ, that could reduce persistence-mediated relapse. Leveraging the sponsor’s, Agnel Sfeir’s, expertise in DNA damage repair and commitment to mentorship, Anne Carpenter’s support of the morphological profiling component, and the training institution’s, Sloan Kettering Institute’s, extensive network of core facilities, cancer-focused seminars, and commitment to supporting postdoctoral fellows, this trainee and project are well-positioned for success. Together, these investigations will provide a thorough and systematic evaluation of DNA repair and morphology in persistence while preparing the trainee for a career as an independent researcher.