Description

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

Shaked Afik¹, Kathleen B. Yates², Kevin Bi², Samuel Darko³, Jernej Godec², Ulrike Gerdemann², Leo Swadling⁴, Daniel C. Douek³, Paul Klenerman⁴, Eleanor J. Barnes⁴, Arlene H. Sharpe², W. Nicholas Haining^2,* and Nir Yosef^1,*

¹UC Berkeley, Berkeley, CA, USA; ²Harvard Medical School, Boston, MA, USA; ³NIAID, NIH, Bethesda, MD, USA; ⁴University of Oxford, Oxford, UK

*Corresponding authors

The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell function at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present a tool to efficiently extract TCR sequence information from short-read scRNA-seq libraries of T cells: TCR Reconstruction Algorithm for Paired-End Single cell (TRAPeS). We apply it to investigate heterogeneity in the CD8⁺ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. We applied TRAPeS to scRNA-seq of CD8⁺ T cells specific for a single epitope from Yellow Fever Virus (YFV). We show that the “naive-like” memory population of YFV-specific CD8⁺ T cells have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype CD8⁺ T cells specific for YFV. This suggests that TCR usage is associated with the differentiation state of the CD8⁺ T cell response to YFV. TRAPeS is publicly available, and can be readily used to investigate the relationship between the TCR repertoire and cellular phenotype.