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 Haining2,* and Nir Yosef1,*
1UC Berkeley, Berkeley, CA, USA; 2Harvard Medical School, Boston, MA, USA; 3NIAID, NIH, Bethesda, MD, USA; 4University of Oxford, Oxford, UK
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.