Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community - Immunologie-Immunopathologie-Immunothérapie
Book Sections Year : 2022

Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community

Abstract

Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) offers the possibility to access the nucleotide sequences of paired receptor chains from T-cell receptors (TCR) or B-cell receptors (BCR). Here we describe two protocols and the downstream bioinformatic approaches that facilitate the integrated analysis of paired T-cell receptor (TR) alpha/beta (TRA/TRB) AIRR-seq, RNA sequencing (RNAseq), immunophenotyping, and antigen-binding information. To illustrate the methodologies with a use case, we describe how to identify, characterize, and track SARS-CoV-2-specific T cells over multiple time points following infection with the virus. The first method allows the analysis of pools of memory CD8 + cells, identifying expansions and contractions of clones of interest. The second method allows the study of rare or antigen-specific cells and allows studying their changes over time.
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hal-03838013 , version 1 (06-04-2024)

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Nidhi Gupta, Ida Lindeman, Susanne Reinhardt, Encarnita Mariotti-Ferrandiz, Kevin Mujangi-Ebeka, et al.. Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community. Immunogenetics, 2453, Springer US, pp.379-421, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2115-8_20⟩. ⟨hal-03838013⟩
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