Integrated single cell analysis identifies CD39 ⁺ tumor-associated NK cells with cytotoxic potential in lung cancer

Despite growing interest in NK cell-targeting immunotherapies for cancer treatment, the transcriptional and functional dynamics of tumor-infiltrating NK cells remain poorly understood. Using matched single-nucleus RNA and ATAC sequencing (snRNA-seq, snATAC-seq), we resolved the heterogeneity of intratumoral NK cells in patients with non-small cell lung cancer (NSCLC). We identified two tumor-associated NK (taNK) cell subsets, marked by ITGAE (CD103) and ITGA1 (CD49a), exhibiting features of circulating NK3 cells and hallmarks of tissue residency, dysfunction, and adaptive NK cells. Subsequent trajectory and regulon analyses revealed that inflammatory signals drive the differentiation of early GZMK⁺ NK3 towards an ENTPD1⁺ (CD39⁺) effector state, characterized by activation of interferon-stimulated genes (ISGs). Functional profiling demonstrated that CD39⁺ taNK cells retain cytotoxic potential which increases upon cytokine stimulation and NKG2A blockade. This study offers mechanistic insights into NK cell differentiation and dysfunction in NSCLC and establishes CD39⁺ taNK cells as a targetable effector population for immunotherapy.