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Updated: Aug 5, 2026
Profiling Sensitivity to Targeted Therapies in EGFR-Mutant NSCLC Patient-Derived Organoids
Published on: November 22, 2021
A single-nucleus transcriptomic characterization of EGFR G719X/S768I double-mutant lung adenocarcinoma identifies an
Chao Zhang1, Lin Liu2, Ruoyu Deng3
1Department of the Second Medical Oncology, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, China; Department of Oncology, Qujing Central Hospital of Yunnan Province / Kunming Medical University Affiliated Qujing Hospital, Qujing, Yunnan, 655000, China.
Abstract:
EGFR double mutations (G719X/S768I) represent a clinically recalcitrant subtype of lung adenocarcinoma (LUAD) characterized by diminished tyrosine kinase inhibitor (TKI) sensitivity. However, the specific tumor microenvironment (TME) features and intercelluar crosstalk driving this therapeutic resistance poorly defined. We performed single-nucleus RNA sequencing (snRNA-seq) on formalin-fixed paraffin-embedded (FFPE) tissues from six EGFR G719X/S768I double-mutant (EGFR_double) and five no EGFR mutation (Non_EGFR) LUAD patients. To provide a comprehensive reference, we integrated our FFPE data with publicly fresh-tissue single cell RNA sequencing (scRNA-seq) data with seven EGFR single-mutant LUAD (EGFR_single) and five adjacent normal (Adjacent), generated a comprehensive atlas of 246,086 cells. Findings were further validated using multiplex immunohistochemistry (mIHC) and pharmacogenomic profiling. We identified a specialized EMT-like malignant subpopulation (MP4) uniquely enriched in EGFR_double, which exhibits a distinct lipid-glycosylation metabolic profile that stabilizes CD44 expression. Cell-cell communication analysis revealed enhanced COL4A3-CD44 interactions between EMT-like malignant MP4 cells and metabolically reprogrammed, immunosuppressive alveolar macrophages in EGFR_double compared with Non_EGFR. MIHC confirmed in situ proximity of this significantly increased COL4A3-CD44 co-localization in EGFR_double. Furthermore, drug sensitivity analysis identified specific vulnerabilities of this subtype. Our study identifies a previously unrecognized malignant-myeloid niche and TME in EGFR_double. These findings provide a translational framework for identifying a potential novel therapeutic targets and suggest that combinatorial strategies targeting the COL4A3-CD44 interaction may overcome therapeutic recalcitrance in this challenging clinical population.
Insights
EGFR double mutations in lung adenocarcinoma create a resistant tumor microenvironment. Researchers identified a novel malignant-myeloid niche and COL4A3-CD44 interactions, suggesting new therapeutic targets for this challenging subtype.
Area of Science:
- Oncology
- Molecular Biology
- Immunology
Background:
- EGFR double mutations (G719X/S768I) confer resistance to tyrosine kinase inhibitors in lung adenocarcinoma (LUAD).
- The tumor microenvironment (TME) and intercellular communication driving this resistance are poorly understood.
Purpose of the Study:
- To elucidate the TME features and cellular crosstalk contributing to therapeutic resistance in EGFR double-mutant LUAD.
- To identify novel therapeutic targets for this recalcitrant LUAD subtype.
Main Methods:
- Single-nucleus RNA sequencing (snRNA-seq) on FFPE tissues from EGFR double-mutant and non-mutant LUAD patients.
- Integration with public fresh-tissue scRNA-seq data for a comprehensive cell atlas.
- Validation using multiplex immunohistochemistry (mIHC) and pharmacogenomic profiling.
Main Results:
- Identification of a unique EMT-like malignant subpopulation (MP4) in EGFR double-mutant LUAD with distinct metabolic profiles.
- Discovery of enhanced COL4A3-CD44 interactions between MP4 cells and immunosuppressive alveolar macrophages.
- Validation of increased COL4A3-CD44 co-localization in EGFR double-mutant tumors.
Conclusions:
- A novel malignant-myeloid niche and TME characterized by COL4A3-CD44 interactions drive therapeutic recalcitrance in EGFR double-mutant LUAD.
- Targeting the COL4A3-CD44 interaction presents a potential strategy to overcome resistance.
- Findings offer a framework for developing new therapies for this challenging patient population.
