Single-cell RNA profiling reveals an immunosuppressive microenvironment in EGFR double-mutant non-small cell lung cancer.

Background: Non-small cell lung cancer (NSCLC) patients with double-driver gene mutations are reported with poorer survival outcomes and reduced therapy responses compared to single-mutant (SM) patients. While substantial progress has been made in treating cancers with single-driver gene alterations, the therapeutic implications and tumor microenvironment of double-mutant (DM) NSCLC remain largely unexplored because of its rarity and poor prognosis. This study aims to delineate the landscape of the immune microenvironment within DM NSCLC. Methods: We employed single-cell RNA sequencing (scRNA-seq) to generate a comprehensive transcriptomic atlas from 25 EGFR mutant NSCLC samples. To assess immune microenvironment changes over time, time-series scRNA-seq and multiplex immunofluorescence analyses were performed in two DM patients. In vitro, EGFR-mutant cell lines were constructed to assess potential therapeutic responses for future clinical applications. Results: The scRNA-seq platform scFocuSCOPE accurately identified and characterized rare, mutation-bearing cancer cells at the single-cell level. DM cancer cells exhibited a strong tendency toward angiogenesis, suggesting an invasive phenotype. DM patients had a more suppressed immune microenvironment, with fewer dysfunctional T lymphocytes. The observation of fewer immune cells and high programmed death ligand-1 (PD-L1) expression in DM cases, probably related to immune evasion and poorer prognosis. In one DM patient, PD-L1 expression remained unchanged after targeted therapy but decreased after immunotherapy. In vitro, EGFR/ERBB2 DM cells showed greater sensitivity to dual-targeted therapies than to single-agent treatments. Conclusions: scFocuSCOPE precisely delineated tumor heterogeneity and immune suppression in EGFR-DM NSCLC. The complex immune landscape of EGFR-DM tumors offers valuable insights for future mechanistic studies and personalized therapies.