Integrative single-cell and computational analysis reveals ligands modulating human gamma delta T cell phenotypes in colorectal cancer 9375

Description γδ T cells, a unique subset of T cells found enriched in the gut epithelium, play an important role in maintaining colon epithelial health and contributing to the anti-tumoral response toward colorectal cancer. Using public single-cell transcriptomic data, we have developed a comprehensive gene expression atlas of γδ T cells in human CRC and confirmed the anti-tumoral activity in various subtypes of γδ T cells, laying a foundation for further exploring their immunotherapeutic use. To address how specific ligands in the tumor microenvironment shape γδ T cell phenotypes and how we can enhance their activation, we first inferred the condition-specific regulatory relationships between transcription factors (TFs) and their target genes in γδ T cells from our integrated data using SCENIC. Then, we integrated the inferred gene regulatory network (GRN) into the known network and used the Personalized PageRank-based algorithm NicheNet to link the differentially expressed genes in each subset of γδ T cells back to their potential upstream ligands. SCENIC predicted 6,951 novel TF-target links from human CRC γδ T cells. Their integration into the known network does not compromise the model’s ability to predict the perturbed ligands in the reference data. Together with PD-L1, ligands including CDHR2 and NECTIN2 may contribute to the exhaustion of CRC γδ T cells. Ligands including S100B, CD7, and CD40LG are predicted to relate to the activation of tissue-resident γδ T cells. Funding Sources This study is supported by an award from the Good Ventures Foundation and Open Philanthropy, as well as start-up funds from Case Western Reserve University and University Hospitals.