Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.

ABSTRACT: T cells recognize antigens and induce specialized gene expression programs (GEPs), enabling functions like proliferation, cytotoxicity and cytokine production. Traditionally, different T cell classes are thought to exhibit mutually exclusive responses, including T_H1, T_H2 and T_H17 programs. However, single-cell RNA sequencing has revealed a continuum of T cell states without clearly distinct subsets, necessitating new analytical frameworks. Here, we introduce T-CellAnnoTator (TCAT), a pipeline that improves T cell characterization by simultaneously quantifying predefined GEPs capturing activation states and cellular subsets. Analyzing 1,700,000 T cells from 700 individuals spanning 38 tissues and five disease contexts, we identify 46 reproducible GEPs reflec

SUBMITTER: Kotliar D 

PROVIDER: S-EPMC12446064 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature