Longitudinal Single-Nucleus Multiomics Reveals Adaptive Programs and Vulnerabilities at Minimal Residual Disease in Oncogene-Driven Lung Cancer

Tyrosine kinase inhibitors (TKI) frequently drive substantial tumor shrinkage in oncogene-driven lung cancer, yet residual cells may persist and seed relapse. To study drug response dynamics, we profiled 46 tumor biopsies from 39 EGFR-mutant lung adenocarcinoma (LUAD) patients receiving osimertinib, including five patients with serial biopsies, using single-nucleus RNA and ATAC sequencing across baseline (n=18), minimal residual disease (MRD) at radiographic nadir (n=11), and progression (n=17). We also profiled nine patient-derived xenograft (PDX) models by single-nucleus RNA sequencing after TKI treatment. MRD showed remodeling of stromal–myeloid compartment and malignant cells which activated ciliary, neural/guidance, mucin-secretory, adhesion, and xenobiotic programs. An MRD-cancer-cell-specific transcriptional signature (NMF_3) was observed in clinical MRD samples and TKI-treated PDX models. FGFR and MUC1-C inhibition enhanced TKI-mediated suppression of residual survival and regrowth in vitro, supporting these pathways as candidate vulnerabilities of the residual-disease state.