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Related Concept Videos

T Cell Activation and Clonal Selection01:22

T Cell Activation and Clonal Selection

854
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...
854
Diversity of Antigen Receptors01:28

Diversity of Antigen Receptors

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Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...
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Related Experiment Video

Updated: Jul 31, 2025

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing
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Quantitative annotations of T-Cell repertoire specificity.

Jiaqi Luo1, Xueying Wang1, Yiping Zou1

  • 1Department of Computer Science, City University of Hong Kong, 83 Tat Tree Ave, Kowloon Tong, Hong Kong, China.

Briefings in Bioinformatics
|May 7, 2023
PubMed
Summary

TCRanno quantifies T-cell receptor (TCR) repertoire specificity, revealing immune changes in infections and diseases. This new method profiles TCRs at multiple levels, aiding personalized immunity insights.

Keywords:
SARS-CoV2TCR repertoire specificitycancercytomegalovirusencoder-classifiersystemic lupus erythematosus

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Area of Science:

  • Immunology
  • Computational Biology
  • Bioinformatics

Background:

  • T-cell receptor (TCR) repertoire specificity is crucial for immune response.
  • Existing methods lack quantitative assessment of TCR repertoire specificity.
  • Understanding TCR specificity is key to personalized immunity.

Purpose of the Study:

  • To develop a computational package, TCRanno, for quantifying TCR repertoire specificity.
  • To infer individual TCR specificity using deep learning and epitope-aware embeddings.
  • To profile TCR repertoire specificity at epitope, antigen, and organism levels.

Main Methods:

  • Developed TCRanno package for quantitative TCR specificity analysis.
  • Utilized deep-learning-based, epitope-aware vector embeddings.
  • Aggregated T-cell receptor clonotype frequencies for quantitative profiling.

Main Results:

  • TCRanno revealed quantitative changes in TCR repertoire specificity across infections, autoimmunity, and cancers.
  • Detected cytomegalovirus-specific TCRs in seronegative individuals, suggesting abortive infections.
  • Identified age-accumulated SARS-CoV-2 specific TCRs in pre-pandemic samples and linked Hepatitis B antigens to lupus.
  • Differentiated TCR repertoires in healthy individuals versus those with melanoma, lung, and breast cancers.

Conclusions:

  • TCRanno provides a quantitative measure of TCR repertoire specificity.
  • The package aids in understanding immune responses to infections, autoimmunity, and cancer.
  • TCRanno is valuable for analyzing single-cell TCR sequencing data and identifying specific T-cells.