Mapping of the T Cell Landscape of Biliary Tract Cancer Unravels Anatomical Subtype-Specific Heterogeneity

Abstract Biliary tract cancer (BTC), encompassing diseases such as intrahepatic (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer (GBC), is not only on the rise but also poses a significant and urgent health threat due to its high malignancy. Genomic differences point to the possibility that these subtypes represent distinct diseases. Elucidation of the specific distribution of T cell subsets, critical to cancer immunity, across these diseases could provide better insights into the unique biology of BTC subtypes and help identify potential precision medicine strategies. To address this, we conducted scRNA-seq and scTCR-seq on CD3+ T cells from 36 samples from 16 BTC patients across all subtypes and analyzed 355 pathological slides to examine the spatial distribution of T cells and tertiary lymphoid structures (TLS). Compared to ICC and GBC, ECC possessed a unique immune profile characterized by T cell exhaustion, elevated CXCL13 expression in CD4+ T helper-like and CD8+CXCL13+ exhausted T cells, more mature TLS, and fewer desert immunophenotypes. Conversely, ICC displayed an inflamed immunophenotype with an enrichment of interferon related pathways and high expression of LGALS1 in activated regulatory T cells, associated with immunosuppression. Inhibition of LGALS1 reduced tumor growth and Treg prevalence in ICC mouse models. Overall, this study unveils T cell diversity across BTC subtypes at the single-cell and spatial level that could open paths for tailored immunotherapies.