Tumor-derived ITGB3 shapes a primed but functionally constrained NK cell state in breast cancer through HLA-E-NKG2A...

Natural killer (NK) cells are vital for anti-tumor immunity, yet their effector functions are frequently constrained within the tumor microenvironment. Integrin β3 (ITGB3) has been implicated in breast cancer progression and stemness, but whether ITGB3 expression in malignant cells influences NK cell states and contributes to immune evasion remains unclear.

Single-cell RNA sequencing data were utilized to profile the transcriptomic and metabolic divergence of NK cells between ITGB3⁺ and ITGB3⁻ tumor microenvironments. Cell-cell communication and pseudotime trajectory analyses were performed to identify key signaling axes. The SCIPAC framework was employed to map single-cell subsets to the bulk TCGA-BRCA cohort for clinical correlation. The mechanistic findings were validated through in vitro co-culture assays and NKG2A blocking experiments using MDA-MB-231 and BT-474 cell lines.

NK cells associated with ITGB3⁺ tumor microenvironments displayed enhanced cytotoxic and inflammatory transcriptional programs, together with metabolic remodeling and stronger clinical associations with advanced TNM stages. Cell-cell communication analysis revealed intensified predicted interactions between ITGB3⁺ malignant cells and NK cells, with enrichment of MHC-I-related signaling and HLA-E-KLRC1/KLRC2 interactions. KLRC1 encodes the inhibitory receptor NKG2A, whereas KLRC2 encodes the activating receptor NKG2C. Therefore, these inferred interactions do not by themselves define the net functional direction of HLA-E signaling. Although KLRC2 was transcriptionally enriched in NK cells from the ITGB3⁺ tumor microenvironment, NKG2A blockade reversed ITGB3-associated suppression of NK-derived IFN-γ secretion, supporting a functional contribution of the inhibitory NKG2A branch.

ITGB3 expression in malignant cells is associated with a primed but functionally constrained NK cell state in breast cancer. Increased malignant-cell HLA-E expression and restoration of IFN-γ production following NKG2A blockade support a functional contribution of the inhibitory NKG2A branch, without excluding concurrent activating signaling through NKG2C.