Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity.

Jason A Carter,Jonathan B Preall,Francois Vigneault,Stephen J Goldfless,Kristina Grigaityte,Adrian W Briggs,Eric Jeffery,Gurinder S Atwal

doi:10.3389/fimmu.2019.01516

Jason A Carter, Jonathan B Preall + Show 6 more

Open Access

https://doi.org/10.3389/fimmu.2019.01516

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Abstract

Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the α and β chain in directing MHC and antigen recognition, repertoire-level immunogenomic analyses have historically examined the β chain alone. To determine the amount of useful information about TCR repertoire function encoded within αβ pairings, we analyzed paired TCR sequences from nearly 100,000 unique CD4+ and CD8+ T cells captured using two different high-throughput, single-cell sequencing approaches. Our results demonstrate little overlap in the healthy CD4+ and CD8+ repertoires, with shared TCR sequences possessing significantly shorter CDR3 sequences corresponding to higher generation probabilities. We further utilized tools from information theory and machine learning to show that while α and β chains are only weakly associated with lineage, αβ pairings appear to synergistically drive TCR-MHC interactions. Vαβ gene pairings were found to be the TCR feature most informative of T cell lineage, supporting the existence of germline-encoded paired αβ TCR-MHC interaction motifs. Finally, annotating our TCR pairs using a database of sequences with known antigen specificities, we demonstrate that approximately a third of the T cells possess α and β chains that each recognize different known antigens, suggesting that αβ pairing is critical for the accurate inference of repertoire functionality. Together, these findings provide biological insight into the functional implications of αβ pairing and highlight the utility of single-cell sequencing in immunogenomics.

Highlights

With potentially up to 1015 unique αβ T cell receptor (TCR) pairs, a wealth of clinically-relevant information pertaining to infectious disease, autoimmunity, and cancer immunotherapy is encoded within the remarkable diversity of the T cell receptors (TCRs) repertoire [1,2,3]
Bipotent T cell precursors differentiate into either the CD4+ helper T cell or the CD8+ cytotoxic T cell lineage. This lineage selection process is contingent upon the interaction of the heterodimeric αβ TCR with either MHC class II or class I, respectively, understanding the general TCR features that mediate the TCRpMHC interaction remains an area of active interest [20, 21]
If αβ TCR pairing is an important component for understanding the differences between two TCR repertoires, we hypothesized that αβ pairs should be much less commonly shared between the CD4+ or CD8+ populations

Summary

Introduction

With potentially up to 1015 unique αβ T cell receptor (TCR) pairs, a wealth of clinically-relevant information pertaining to infectious disease, autoimmunity, and cancer immunotherapy is encoded within the remarkable diversity of the TCR repertoire [1,2,3]. As limitations in technology have historically precluded meaningful single-cell sequencing experiments, our current understanding of the TCR repertoires’ diversity, structure, and function is almost entirely based on bulksequencing of the β chain repertoire alone [4,5,6]. Our study demonstrates the utility of using new single-cell sequencing approaches, in addition to conventional high-throughput bulk-sequencing, to capture a more accurate picture of TCR repertoire function

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