Abstract B093: Combinatorial CRISPR screening reveals synthetic lethal and suppressor interactions in RTK signaling and glycosylation networks
TL;DR
The N-glycosylation module is demonstrated as a recurrent hub of context-dependent genetic interactions and combinatorial CRISPR screening as a scalable approach for identifying therapeutic targets and resistance mechanisms in oncogene-driven cancers.
Abstract
Oncogenic contexts shape synthetic lethal vulnerabilities and suppressor interactions that underlie drug resistance mechanisms, yet this context-dependence remains poorly characterized. Combinatorial CRISPR screens offer a principled approach to surface these interactions at scale with direct implications for therapeutic targeting and drug combination strategies. Using the In4mer 4-plex Cas12a knockout platform, we screened pairwise genetic interactions across RTK signaling and glycosylation networks in oncogene-stratified cancer cells (Lin et al., BioRxiv 2025), identifying hits enriched in the glycosylation machinery. Building on these findings, focused validation screens across cancer cell lines with KRAS-, BRAF-, and EGFR-drivers confirm high-effect genetic interactions concentrated in the glycosylation module across oncogenic backgrounds, revealing both synthetic lethal dependencies and suppressor interactions. Synthetic lethal candidates linking ER stress regulation and glycosyltransferase activity were supported by dependency-expression correlations in cancer cell lines, and recurrent amplification of glycosylation machinery in patient tumors is associated with poor clinical outcomes. Preliminary cell-based validation assays further corroborate a suppressor interaction, implicating a potential resistance mechanism to EGFR inhibition. Together, these findings demonstrate the N-glycosylation module as a recurrent hub of context-dependent genetic interactions and combinatorial CRISPR screening as a scalable approach for identifying therapeutic targets and resistance mechanisms in oncogene-driven cancers. Subin Kim, Chenchu Lin, Sabriyeh Alibai, Iulia Veronica Gheorghe, Jui Hsuan Chou, Traver Hart. Combinatorial CRISPR screening reveals synthetic lethal and suppressor interactions in RTK signaling and glycosylation networks [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr B093.