Titre

T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps.

Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Andreatta, M.
Auteure/Auteur
Gueguen, P.
Auteure/Auteur
Borcherding, N.
Auteure/Auteur
Carmona, S.J.
Auteure/Auteur
Liens vers les personnes
Liens vers les unités
ISSN
2331-8325
Statut éditorial
Publié
Date de publication
2023-08-20
Volume
13
Numéro
16
Première page
e4735
Peer-reviewed
Oui
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
T cells are endowed with T-cell antigen receptors (TCR) that give them the capacity to recognize specific antigens and mount antigen-specific adaptive immune responses. Because TCR sequences are distinct in each naïve T cell, they serve as molecular barcodes to track T cells with clonal relatedness and shared antigen specificity through proliferation, differentiation, and migration. Single-cell RNA sequencing provides coupled information of TCR sequence and transcriptional state in individual cells, enabling T-cell clonotype-specific analyses. In this protocol, we outline a computational workflow to perform T-cell states and clonal analysis from scRNA-seq data based on the R packages Seurat, ProjecTILs, and scRepertoire. Given a scRNA-seq T-cell dataset with TCR sequence information, cell states are automatically annotated by reference projection using the ProjecTILs method. TCR information is used to track individual clonotypes, assess their clonal expansion, proliferation rates, bias towards specific differentiation states, and the clonal overlap between T-cell subtypes. We provide fully reproducible R code to conduct these analyses and generate useful visualizations that can be adapted for the needs of the protocol user. Key features Computational analysis of paired scRNA-seq and scTCR-seq data Characterizing T-cell functional state by reference-based analysis using ProjecTILs Exploring T-cell clonal structure using scRepertoire Linking T-cell clonality to transcriptomic state to study relationships between clonal expansion and functional phenotype Graphical overview.
Sujets

Reference projection

Single-cell analysis

T-cell clone

T-cell receptor

Tcr

Transcriptomics

scRNA-seq

scTCR-seq

TCR

PID Serval
serval:BIB_5A2CCFDDD06A
DOI
PMID
WOS
Permalien
Date de création
2023-09-20T10:58:39.973Z
Date de création dans IRIS
2025-05-20T18:31:02Z
Fichier(s)
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Vignette d'image
Nom

37638293_BIB_5A2CCFDDD06A.pdf

Version du manuscrit

published

Licence

https://creativecommons.org/licenses/by/4.0

Taille

1.42 MB

Format

Adobe PDF

PID Serval

serval:BIB_5A2CCFDDD06A.P001

URN

urn:nbn:ch:serval-BIB_5A2CCFDDD06A3

Somme de contrôle

(MD5):0c482a9a7f6e6c7d5b27c631a1e825fd