Abstract 1874: Common vulnerabilities of stem cells along the Barrett's-dysplasia-adenocarcinoma sequence

Abstract Barrett's esophagus (BE) is an early precursor of esophageal adenocarcinoma and therefore a relevant target of preemptive therapeutics. Using robust stem cell cloning technologies, we have cloned stem cells from patient-matched biopsies of BE, low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinoma (EAC) from multiple patients. Whole exome sequencing of these stem cells reveals the mutational maturation along the sequence of BE, LGD, HGD, and EAC at unprecedented resolution of both copy number and single nucleotide variation. In vitro differentiation and xenografting of these clones recapitulates their original histology and shows that only the EAC stem cells yield robust tumors in immunodeficient mice. Leveraging the intrinsic immortality of these stem cells, we have performed high-throughput screens for small molecules that selectively kill BE stem cells without harming patient-matched normal esophageal stem cells. These screening efforts evolved into synthetic lethal strategies that identified drug combinations that selectively eliminate, in vitro, BE stem cells from 20 of 23 cases. Remarkably, this same synthetic lethal drug combination also eliminated in vitro stem cells of LGD, HGD, and EAC that were not components of the original screens. We have used synthetic chemistry to generate a series of novel molecules based on the identified drug combination that significantly improved the in vitro efficacy to sub-nanomolar levels. These novel molecules directed to the stem cell component of BE, LGD, HGD, and EAC also show potent effects against tumors generated from EAC stem cells in immunodeficient mice. We anticipate that these synthetically lethal drug combinations will have potential utility against precursor lesions to preempt EAC as well as against EAC itself. Citation Format: Wa Xian, Frank McKeon, Christopher Crum, Jaffer Ajani, Peter Davies, Matthew Vincent, William Bachovchin, Hung-Sen Lai, Shuang Pan, Amber Su, Ashley Hoffman, Raul Caballero Montes, Melina Khorrami, Melika Khorrami, Yusuke Yamamoto. Common vulnerabilities of stem cells along the Barrett's-dysplasia-adenocarcinoma sequence [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 1874.