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

Massimo Andreatta, Paul Gueguen, Nicholas Borcherding, Santiago J. Carmona

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

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.

Original languageEnglish
Article numbere4735
JournalBio-protocol
Volume13
Issue number16
DOIs
StatePublished - Aug 20 2023

Keywords

  • Reference projection
  • scRNA-seq
  • scTCR-seq
  • Single-cell analysis
  • T-cell clone
  • T-cell receptor
  • TCR
  • Transcriptomics

Fingerprint

Dive into the research topics of 'T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps'. Together they form a unique fingerprint.

Cite this