Multimodal profiling of HER2/neu-specific TCR-T cells reveals clonotype-dependent activation programs underlying differential cytotoxic efficacy

In this study, we combine functional assays with multimodal single-cell and bulk profiling to identify functional diversity among TCR-engineered T cells targeting the HER2/neu antigen. We focus on a set of three TCR clonotypes that recognize the HER2/neu-derived peptide KIFGSLAFL. By analyzing these clonotypes side by side in cytotoxicity tests, both in vitro and in vivo, at single-cell resolution by integrating their gene and protein expression, by bulk Nanostring transcriptomics, and LegendPlex secretomics, we aimed to identify the molecular programs that distinguish a highly effective anti-HER2/neu T cell clonotype from a less effective one.