High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8⁺T cells

Abstract

Although critical to T cell function, antigen specificity is often omitted in high-throughput multi-omics based T cell profiling due to technical challenges. We describe a high-dimensional, tetramer-associated T cell receptor sequencing (TetTCR-SeqHD) method to simultaneously profile TCR sequences, cognate antigen specificities, targeted gene-expression, and surface-protein expression from tens of thousands of single cells. Using polyclonal CD8+ T cells with known antigen specificity and TCR sequences, we demonstrated over 98% precision for detecting the correct antigen specificity. We also evaluated gene-expression and phenotypic differences among antigen-specific CD8+ T cells and characterized phenotype signatures of influenza- and EBV-specific CD8+ T cells that are unique to their pathogen targets. Moreover, with the high-throughput capacity of profiling hundreds of antigens simultaneously, we applied TetTCR-SeqHD to identify antigens that preferentially enrich cognate CD8+ T cells in type 1 diabetes patients compared to healthy controls, and discovered a TCR that cross reacts between diabetic and microbiome antigens. TetTCR-SeqHD is a powerful approach for profiling T cell responses.

Antigen-Specific Treg Therapy in Type 1 Diabetes – Challenges and Opportunities

“…research to study individual heterogeneity, drug resistance, or disease progression at an unprecedented level (47,48). Especially, T cell focused immunological studies will benefit from recent developments as newly arising techniques can also simultaneously reconstruct TCR sequences and determine their specificities for a predefined set of epitopes (49)(50)(51). These methods have already greatly advanced our understanding of T cell responses in disease (50,(52)(53)(54)(55)(56), and lead to innovative analysis strategies such as the usage of TCR-sequence as natural barcodes to trace the cellular response pre-and post-antigen stimulation in vivo (57).…”