Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy.

Anna Pasetto,Yong-Chen Lu

doi:10.3389/fimmu.2021.689091

Abstract

T cells have been known to be the driving force for immune response and cancer immunotherapy. Recent advances on single-cell sequencing techniques have empowered scientists to discover new biology at the single-cell level. Here, we review the single-cell techniques used for T-cell studies, including T-cell receptor (TCR) and transcriptome analysis. In addition, we summarize the approaches used for the identification of T-cell neoantigens, an important aspect for T-cell mediated cancer immunotherapy. More importantly, we discuss the applications of single-cell techniques for T-cell studies, including T-cell development and differentiation, as well as the role of T cells in autoimmunity, infectious disease and cancer immunotherapy. Taken together, this powerful tool not only can validate previous observation by conventional approaches, but also can pave the way for new discovery, such as previous unidentified T-cell subpopulations that potentially responsible for clinical outcomes in patients with autoimmunity or cancer.

Highlights

A T-cell receptor (TCR) is a heterodimer consisting of two chains, TCRa and TCRb chains, that allow the recognition of peptides in the contest of major histocompatibility complex (MHC) molecules
Each of the two chains is made of a variable region and a constant region that are spliced together during the T cell development that happens in the thymus
While CDR1 and CDR2 are encoded by the V segment, the CDR3 regions results from the juxtaposition of the V, (D) and J

Summary

INTRODUCTION

A T-cell receptor (TCR) is a heterodimer consisting of two chains, TCRa and TCRb chains, that allow the recognition of peptides in the contest of major histocompatibility complex (MHC) molecules. Micromanipulation, FACS sort and microfluidics techniques, multiplex PCR and full-length cDNA amplification approach can be used to perform single-cell TCR and transcriptome sequencing. An example is TraCeR, a computational method that allows to reconstruct the variable sequence of TCRa and TCRb chains through use of a “combinatorial recombinome” library of all possible TCR sequences, this method was initially used in combination with the FluidigmC1 System [31, 32] Another computational method is “single-cell TCRseq” [33] that employs several consecutive steps to first identify and count RNA reads mapping to specific TCR V and C regions, perform multiple alignments to create consensus V and C gene sequences. The microdroplet approach is less sensitive to detect low abundant genes, this

Multiplex PCR

SPATIAL TRANSCRIPTOMICS

Screening of Antigenic Libraries

The Role of T Cells in Infectious Diseases

CAVEATS ON EXPERIMENTAL DESIGN AND DATA INTERPRETATION