380: Prime-SGE maps drug-resistance variants at scale

Abadie FMC et al., Cell Genomics - Abadie et al. present prime‑SGE, a pooled prime‑editing framework that installs thousands of precise point mutations across multiple oncogenes and identifies drug‑resistance variants by sequencing integrated pegRNAs after positive‑selection with kinase inhibitors. The method resolved known resistance mutations (e.g., EGFR C797S, KRAS G12 variants), uncovered less-characterized candidates, compared resistance landscapes across covalent and non‑covalent EGFR inhibitors, and validated resistant edits in vivo. Key terms: prime editing, drug resistance, EGFR, KRAS, multiplex screening. Study Highlights:Prime‑SGE uses libraries of barcoded pegRNAs/epegRNAs delivered at low MOI into PEmax‑expressing, MLH1‑knockout cell lines to program thousands of point mutations and read out variant abundance by sequencing integrated guides after drug selection. In pooled screens across eight oncogenes and three EGFR inhibitors, prime‑SGE recovered established resistance mutations (EGFR C797S, KRAS G12 variants) and identified less-characterized hits (e.g., EGFR Q791, Y801). Distinct resistance landscapes emerged for covalent versus non‑covalent EGFR inhibitors, and barcodes showed many resistant clones arose from independent editing events. Prime‑edited resistant cells formed tumors in osimertinib-treated xenografts, demonstrating in vivo relevance. Conclusion:Prime‑SGE enables scalable, positive‑selection profiling of thousands of precise point mutations across the genome to identify and compare drug‑resistance variants, though sensitivity is limited by variable prime editing efficiency. The approach can prioritize resistance variants for follow-up and inform inhibitor development and choice. Music:Enjoy the music based on this article at the end of the episode. Article title:A multiplex, prime editing framework for identifying drug resistance variants at scale First author:Abadie FMC Journal:Cell Genomics DOI:10.1016/j.xgen.2026.101167 Reference:Abadie FMC, Suiter CC, Smith NT, et al. A multiplex, prime editing framework for identifying drug resistance variants at scale. Cell Genomics. 2026;6:101167. doi:10.1016/j.xgen.2026.101167 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/prime-sge-drug-resistance-variants QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-05-29. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited the transcript's sections describing Prime-SGE concept, the scale of edits, key resistance mutations (EGFR C797S, KRAS G12 variants, Q791, Y801), inhibitor contexts (osimertinib, sunvozertinib, CH7233163), in vivo xenograft validation, and limitations (editing efficiency, false negatives). QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- Prime-SGE enables multiplexed installation of thousands of precise edits across multiple genes with readout by integrated pegRNA barcodes- Large-scale scr...