A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires.

Area of Science:

• Immunology
• Bioinformatics
• Molecular Biology

Background:

• Current T cell monitoring methods lack multiplexity and sensitivity.
• Deep sequencing of T Cell Receptor (TCR) repertoires offers a global view but antigen specificity assignment is a bottleneck.

Purpose of the Study:

• To develop a novel framework for identifying antigen-specific T cell responses using deep TCR sequencing.
• To overcome the limitations of current methods in assigning antigen specificities within complex T cell repertoires.

Main Methods:

• Combined antigen-driven expansion, deep TCR sequencing, and a novel computational analysis framework.
• Identified homologous 'Clusters of Expanded TCRs (CETs)' without requiring cell isolation.
• Assigned antigen specificities to identified CETs against a background of non-specific T cell clones.

Main Results:

• Demonstrated that clonotypes within each CET are reactive to the same epitope.
• Showed that protein antigens stimulate multiple CETs, each reactive to constituent peptides.
• Successfully assigned antigen-specificity to rare T cell clones within diverse, uncultured repertoires.

Conclusions:

• The novel analysis framework enables confident identification and antigen assignment of homologous CETs.
• This method provides high-fidelity monitoring of T cell responses to vaccination and immunotherapy.
• The approach advances the ability to understand and track cellular immune responses in personalized medicine.