Abstract 3363: LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo
Authors: Lauren Martires, Leanne G. Ahronian, Charlotte Pratt, Nikitha Das, Xiaobin Zhang, Douglas A. Whittington, Hongxiang Zhang, Binzhang Shen, Jon Come, Patrick McCarren, Mu-Sen Liu, Chengyin Min, Tianshu Feng, Haris Jahic, Eric Brophy, Daniel Aird, Jannik N. Andersen, Alan Huang, Fang Li, William D. Mallender, Hilary E. Nicholson
Journal: Cancer Research (2024)

Abstract Women harboring a mutation in the BRCA1 gene have a &amp;gt;7X increased risk of developing breast cancer and &amp;gt;35X increased risk of developing ovarian cancer in their lifetime compared to women lacking such mutations. While PARP1/2 inhibitors are efficacious in the BRCA mutant setting, this efficacy is limited and resistance develops readily. Additional therapeutic targets beyond PARP1/2 are needed to treat cancer patients with BRCA mutations. We performed CRISPR screens in 11 BRCA1/2 wild-type and 2 BRCA1 mutant cancer cell lines to identify targets that are synthetic lethal with BRCA1 mutations. In addition to USP1, PARP1 and POLQ, we identified the DNA ligase gene LIG1 as a novel target that when knocked out kills BRCA1 mutant cells selectively. Internal analysis of BRCA mutations in breast and ovarian cancer cell lines in the Project Achilles database further validated the hyperdependence of BRCA1 mutant cells on LIG1. Single-gene perturbation of LIG1 using CRISPRn, CRISPRi, and RNAi confirm the lethal effect of LIG1 inactivation in BRCA1 mutant cell lines, but not BRCA1/2 wild-type cell lines. This loss of viability could be rescued by complementing with an exogenous wild-type LIG1 cDNA, demonstrating the on-target nature of the genetic tools. Using a degradable DNA Ligase I fusion protein, we demonstrate a strong correlation between DNA Ligase I protein level and viability in BRCA1 mutant cells. Enzymatically inactive DNA Ligase I mutant protein (LIG1K568A) was unable to rescue the loss of viability caused by endogenous LIG1 depletion supporting the tractability of this target from a small molecule inhibitor perspective. These data were reproduced in vivo using BRCA1 mutant MDA-MB-436 derived tumors, in which tumor growth was inhibited &amp;gt;80% upon loss of LIG1.Mechanistically, DNA ligase I plays a critical role in DNA replication and damage repair by sealing nicks in the phosphodiester backbone of DNA. When these nicks are not repaired, they are marked by the addition of PAR chains. Consistent with this mechanism, we demonstrated that inactivation of LIG1 leads to increased PARylation. The induction of PARylation was proportional to the level of inactivation of LIG1 protein, supporting a correlation between LIG1 activity and DNA nick repair. Together, these data support DNA ligase I as a synthetic lethal target in the context of BRCA1 mutations. Citation Format: Lauren Martires, Leanne G. Ahronian, Charlotte Pratt, Nikitha Das, Xiaobin Zhang, Douglas A. Whittington, Hongxiang Zhang, Binzhang Shen, Jon Come, Patrick McCarren, Mu-Sen Liu, Chengyin Min, Tianshu Feng, Haris Jahic, Eric Brophy, Daniel Aird, Jannik N. Andersen, Alan Huang, Fang Li, William D. Mallender, Hilary E. Nicholson. LIG1 inactivation selectively inhibits growth of BRCA1 mutant cells in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3363.