Investigations of Loss of Heterozygosity–Associated Dependencies in Cancer

Abstract

Alterations in non-driver genes represent an emerging class of potential therapeutic targets in cancer. Most tumors undergo loss of heterozygosity (LOH) of hundreds to thousands of non-driver genes, generating discrete differences between tumor and normal cells. However, only a small body of research examines how these differences can be used as the basis for cancer therapies. To address this issue, we interrogated LOH of polymorphisms in essential genes as a novel class of therapeutic targets. We hypothesized that monoallelic inactivation of the allele retained in tumors can selectively kill cancer cells but not somatic cells, which retain both alleles. We term this class GEMINI vulnerabilities after the twins from Greek mythology, Castor and Pollux, one of whom was mortal and other immortal. To study these vulnerabilities, we first performed a large-scale analysis of germline variant, gene essentiality, and LOH data to identify potential GEMINI vulnerabilities. This analysis identified 5664 variants in 1278 essential genes that undergo LOH in cancer. Second, we performed proof-of-concept validation of GEMINI vulnerabilities in two essential genes, PRIM1and EXOSC8. We demonstrated that allele-specific inactivation of either of these genes reduced growth of cells harboring the targeted allele, while cells harboring the non-targeted allele remain intact. Finally, we evaluated the potential for each GEMINI variant to be targeted using allele-specific gene-editing, RNAi, or small-molecule approaches. These analyses indicated that not all GEMINI vulnerabilities may be ideal candidates for RNAi-based therapeutics. Nonetheless, we identified several promising GEMINI vulnerabilities for future efforts to develop allele-specific small-molecule inhibitors. This work rigorously validates GEMINI vulnerabilities as a potential class of therapeutic targets and defines its potential scope. These findings provide a strong starting point for future development of therapeutic agents targeting GEMINI vulnerabilities.