Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions

ABSTRACT: T cell receptors (TCR) and gene expression provide two complementary and essential aspects in T cell understanding, yet their diversity presents challenges in integrative analysis. We introduce TCRclub, a novel method integrating single-cell RNA sequencing data and single-cell TCR sequencing data using local harmony to identify functionally similar T cell groups, termed 'clubs'. We applied TCRclub to 298,106 T cells across seven datasets encompassing various diseases. First, TCRclub outperforms the state-of-the-art methods in clustering T cells on a dataset with over 400 verified peptide-major histocompatibility complex categories. Second, TCRclub reveals a transition from activated to exhausted T cells in cholangiocarcinoma patients. Third, TCRclub discovered the pathways that could inter

SUBMITTER: Ms Yiping Zou 

PROVIDER: S-SCDT-10_1038-S44320-024-00070-5 | biostudies-other |

REPOSITORIES: biostudies-other