Leveraging the adaptive NKG2C-HLA-E axis using neural network identified peptides for HER2-targeted NK cell immunotherapy 2334737

Abstract Introduction Breast cancer remains a leading cause of cancer-related mortality globally, with HER2+ tumors representing 15-20% of cases further complicated by treatment resistance. As a novel treatment approach, natural killer (NK) cells are ideal antitumoral effectors that circumvent MHC restriction and T-cell therapy associated toxicities. Although recognized as innate effectors, subsets of NK cells called adaptive NK (aNK) cells show antigen-specific memory responses via the NKG2C-HLA-E axis. In this study, we identify HER2-derived peptides that preferentially engage aNK cell responses through the NKG2C-HLA-E axis. Methods Top-scoring peptides were identified from HER2 using neural network—based HLA-E binding models trained on HLA-E variants and NKG2C/NKG2A-specific peptides and compared to reference HLA-E stabilizing peptides using root mean square deviation. Selected peptides were evaluated for in vitro HLA-E stabilization in K562-HLA-E*01:01 cells. NK cell responses from healthy CD3-depleted peripheral blood mononuclear cells (PBMCs) were assessed by intracellular cytokine staining (ICS) following 6-hour peptide stimulation. Results In-silico screening identified three HER2-derived nonamer peptides: PQL, SFVQ, and LLD, with the potential to stabilize HLA-E and preferentially engage NKG2C. In vitro stabilization assays confirmed robust peptide-dependent surface expression of HLA-E compared to DMSO on K562-HLA-E*01:01 cells after peptide stimulation. ICS assay revealed increased CD107a expression on NKG2C+ NK cells compared to NKG2A+ NK cells post peptide-stimulation, indicating NKG2C-mediated cytotoxic responses against HER2 peptides. Conclusion Our findings indicate that HLA-E stabilizing HER2-derived peptides can specifically and robustly activate NKG2C-mediated cytotoxic NK responses in healthy donors. Additional clinical evaluations will be required, but these findings suggest NKG2C-mediated immunotherapeutics may represent attractive personalized therapies for HER2+ breast and other cancers. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)