Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing

Highlights

• Single-cell RNA-seq reveals distinctive functional composition of T cells in HCC

• Clonal enrichment of infiltrating Tregs and exhausted CD8 T cells in HCC

• LAYN is linked to the suppressive function of tumor Treg and exhausted CD8 T cells

• Combined expression and TCR-based analyses show connectivity among T cell subsets

Summary

Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8⁺ T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8⁺ T cells and Tregs and represses the CD8⁺ T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.