Abstract 1156: Real-world clinical multi-omics analyses reveal bifurcation of ER-independent and ER-dependent drug resistance to CDK4/6 inhibitors

Abstract To better understand the molecular mechanisms of drug resistance to CDK4/6 inhibitors (CDK4/6i) and inform precision medicine strategies, we retrospectively analyzed a multi-omics dataset of 400 HR+/HER2- mBC patients who received CDK4/6i plus endocrine therapies in routine clinical practice, including 200 pre-treatment (Pre), 227 post-progression (Post) samples. Integrative clustering analysis identified three subgroups of tumors harboring different drug resistance mechanisms: ER driven, ER co-driven and ER independent. The ER independent subgroup increased the most in prevalence from 4% pre-treatment to 23% post-progression and is characterized by down-regulation of estrogen signaling and enrichment of drug resistance markers including TP53 and RB1 mutations, Basal-like and Her2-like subtypes and CCNE1 over-expression. We deconvoluted bulk tumor expression profiles to derive cancer-specific expression (CSE) profiles for investigating tumor intrinsic mechanisms that give rise to ER independent drug resistance. We then performed trajectory inference analyses often used in single-cell transcriptomics on CSEs and identified a latent pseudotime variable strongly correlated with ER independence and disease progression. Elastic principal graph (EPG) analysis further revealed bifurcated evolutionary trajectories for drug resistance that correspond to ER-dependent vs. ER-independent mechanisms. Using elastic net models trained on in vitro CRISPR knockout screen data, we predicted a shift in therapeutic dependency on ESR1 and CDK4 among ER-dependent tumors to CDK2 among ER-independent tumors. These predictions were experimentally validated using genetically modified isogenic models. Citation Format: Zhengyan Kan, Ji Wen, Vinicius Bonato, Jennifer Webster, Wenjing Yang, Vladimir Ivanov, Kimberly Hyunjung Kim, Whijae Roh, Chaoting Liu, Xinmeng Jasmine Mu, Jennifer Lapira-Miller, Jon Oyer, Todd VanArsdale, Paul A. Rejto, Jadwiga Bienkowska. Real-world clinical multi-omics analyses reveal bifurcation of ER-independent and ER-dependent drug resistance to CDK4/6 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1156.