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T Cell Activation and Clonal Selection

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...

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Related Experiment Video

Updated: Aug 20, 2025

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry

Published on: June 26, 2018

Systematic single-cell pathway analysis to characterize early T cell activation.

Jack A Bibby¹, Divyansh Agarwal², Tilo Freiwald³

¹Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

|November 23, 2022

Summary

We developed single-cell pathway analysis (SCPA), a new R package for analyzing omics data. SCPA effectively reveals T-cell activation pathways, including interferon systems and arachidonic acid metabolism, enhancing cellular process understanding.

Keywords:

CP: Immunology SCPA T cell arachidonic acid cytokines gene set metabolism pathway analysis single-cell RNA-seq single-cell pathway analysis type I interferon

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Area of Science:

Computational Biology
Immunology
Genomics

Background:

Pathway analysis is crucial for interpreting omics data and identifying cellular process alterations.
Existing methods may lack sensitivity or flexibility for complex biological datasets.

Purpose of the Study:

To introduce the open-source R package single-cell pathway analysis (SCPA).
To provide a sensitive, distribution-free framework for multisample distribution testing in single-cell omics data.
To characterize pathway activity during T-cell activation and across different tissues.

Main Methods:

Implementation of a novel statistical framework in the SCPA R package.
Generation and analysis of a single-cell RNA sequencing (scRNA-seq) T-cell dataset.
Comparison of SCPA's effectiveness against commonly used pathway analysis methods.

Main Results:

SCPA demonstrated superior performance compared to existing methods.
Characterization of T-cell activation revealed an intrinsic type I interferon system regulating T-cell survival.
Arachidonic acid metabolism was identified as critical throughout T-cell activation.
Alpha-defensin expression was highlighted as a marker for bone-marrow-derived T-cells.

Conclusions:

SCPA offers a powerful and widely applicable tool for single-cell pathway analysis.
The study identified key regulatory pathways involved in T-cell survival, activation, and tissue-specific characteristics.
This work advances the understanding of T-cell biology through systems-level pathway activity characterization.