Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data.

Yu Bai,Janelle Waite,Yi Wei,Ying Huang,Wentian Li,Natasha Levenkova,Chunguang Guo,Lynn E Macdonald,Wen Fury,Kurt H Edelmann,Xuan Ye,Dimitris Skokos,Thomas Barry,David Wang

doi:10.1371/journal.pone.0207020

Abstract

Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping error. In addition, only a small percentage of the genome-wide reads may cover the TCR loci and thus the repertoire could be significantly under-sampled. Although this approach has been applied in a few studies, the utility of transcriptome sequencing in probing TCR repertoires has not been evaluated extensively. Here we present a systematic assessment of RNA-Seq in TCR profiling. We evaluate the power of both Fluidigm C1 full-length single cell RNA-Seq and bulk RNA-Seq in characterizing the repertoires of different diversities under either naïve conditions or after immunogenic challenges. Standard read length and sequencing coverage were employed so that the evaluation was conducted in accord with the current RNA-Seq practices. Despite high sequencing depth in bulk RNA-Seq, we encountered difficulty quantifying TCRs with low transcript abundance (<1%). Nevertheless, top enriched TCRs with an abundance of 1–3% or higher can be faithfully detected and quantified. When top TCR sequences are of interest and transcriptome sequencing is available, it is worthwhile to conduct a TCR profiling using the RNA-Seq data.

Highlights

T-cell receptors (TCR), usually consisting of disulfide-bound α and β chains, are expressed on the surface of T lymphocytes and play a vital role in antigen-induced T cell immunity [1]
We only focused on in-frame/productive V-CDR3-J recombination
Because the acute lymphocytic choriomeningitis virus (LCMV) infection is known to induce a potent antigen-specific expansion [5], we evaluated the bulk RNA-Seq using T cells retrieved from the LCMV-challenged mice versus those from naïve mice as the expanded and non-expanded repertoires, respectively. 5’RACE targeted TCR amplicon sequencing was applied to the same bulk samples for comparison

Summary

Introduction

T-cell receptors (TCR), usually consisting of disulfide-bound α and β chains, are expressed on the surface of T lymphocytes and play a vital role in antigen-induced T cell immunity [1]. A large repertoire of diverse TCRs enables T cells to recognize a wide variety of antigens displayed by major histocompatibility complex (MHC) molecules. TCRs promote a series of signaling cascades that regulate T cell activation, cytokine production, survival and proliferation [2, 3]. Clonal expansion of reactive T cells may occur and reshape the repertoire [4]. As a key component of T cell specificity, the TCR.

Methods

Results

Conclusion