A Ligand-Centered Framework for γδ T Cell Activation in Colorectal Cancer Revealed by Single-Cell and Transformer-Based Perturbation

Understanding the activation mechanisms of {gamma}{delta} T cells in colorectal cancer (CRC) is critical for harnessing their therapeutic potential. Here, using an atlas of human CRC-infiltrating {gamma}{delta} T cells that we built by integrating multiple single-cell RNA-seq datasets, we developed a {gamma}{delta} T cell-refined ligand inference pipeline by combining differential gene expression, gene regulatory network prediction, ligand inference, and in silico perturbation analysis. This approach identified IL-15 and TNFSF9 (4-1BBL) as candidate ligands promoting {gamma}{delta} T cell effector function, and highlighted NCR2 and KLRC3 (NKG2E), whose in silico overexpression was associated with {gamma}{delta} T cell activation. Ligand enrichment analyses further indicated that monocytes and dendritic cells are key contributors to {gamma}{delta} T cell activation within the tumor microenvironment. Together, our results offer a systems-level view of the signaling and transcriptional programs governing {gamma}{delta} T cell phenotypes in CRC and provide a foundation for {gamma}{delta} T cell-based immunotherapies with enhanced antitumor function.