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Related Concept Videos

T Cell Activation and Clonal Selection01:22

T Cell Activation and Clonal Selection

T cells are integral to our adaptive immune system, recognizing and effectively responding to foreign antigens. T cell activation and clonal selection are pivotal in orchestrating this immune response. This article elucidates these mechanisms, detailing the roles of cluster of differentiation (CD) markers, major histocompatibility complex (MHC) molecules, costimulatory signals, and the process of clonal selection.
Naive T cells that have not yet encountered an antigen express two primary CD...
T Cell Types and Functions01:24

T Cell Types and Functions

When T cells with CD4 markers are activated, they give rise to two types of effector cells: helper T cells and regulatory T cells. Meanwhile, T cells with CD8 markers differentiate into effector cytotoxic T cells. The differentiation of CD4 T cells into helper T cell subsets, such as Th1, Th2, and Th17 cells, is dependent on the antigen type, antigen-presenting cell, and regulatory cytokines.
Th1 cells stimulate dendritic cells to express necessary co-stimulatory molecules on their surfaces for...

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An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution.

Wen-Kang Shen1, Chu-Yu Zhang1, Yi-Min Gu2

  • 1Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China; Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.

Science Bulletin
|March 29, 2025
PubMed
Summary

Researchers created the largest human T cell reference atlas and a tool (STCAT) for precise T cell subtype annotation. This advances understanding of T cell immunity in diseases like cancer and COVID-19.

Keywords:
Annotation toolDatabaseReferenceT cell subtypes and statesT cellsscRNA-seq

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Area of Science:

  • Immunology
  • Genomics
  • Computational Biology

Background:

  • T cells exhibit diverse subtypes and functional states crucial for immune responses.
  • Lack of comprehensive reference atlases and automated annotation tools hinders T cell research.
  • Analyzing T cell heterogeneity is vital for understanding various physiological and pathological conditions.

Purpose of the Study:

  • To construct the largest human T cell reference dataset to date.
  • To develop an automated tool (STCAT) for accurate T cell subtype and state annotation from scRNA-seq data.
  • To facilitate deeper insights into T cell immunity in cancer and infectious diseases.

Main Methods:

  • Compiled a reference dataset of 1,348,268 T cells from 35 conditions and 16 tissues.
  • Classified T cells into 33 subtypes and 68 categories using hierarchical models and marker correction.
  • Developed and validated the STCAT tool on independent scRNA-seq datasets, comparing its accuracy to existing methods.

Main Results:

  • STCAT demonstrated 28% higher accuracy than existing tools in T cell annotation.
  • Identified enrichment of CD4+ Th17 cells in late-stage lung cancer and MAIT cells in mild COVID-19.
  • Revealed decreased Treg cytotoxicity in post-treatment ovarian cancer and distinct CD4+/CD8+ T cell distributions in tumor vs. healthy samples.

Conclusions:

  • The developed human T cell reference atlas and STCAT tool significantly enhance T cell research capabilities.
  • These resources provide a foundation for analyzing T cell immunity in diverse conditions, including cancer immunology.
  • The TCellAtlas database offers a platform for exploring T cell expression and analyzing custom scRNA-seq data.