Advancements in single cell multiomic profiling of antigen-specific T cells with dCODE Dextramer&[trade] (RiO) and BD® AbSeq Reagents on the BD Rhapsody&[trade] Single-Cell Analysis System

Abstract The advancement of immunotherapies and drug development relies on the characterization of antigen-specific T cells. However, due to their low frequency among T cells and their inherent weak affinity to bind known MHC-peptide complexes, detection of these cells has been difficult. Furthermore, pairing this information with the corresponding variable (V), diversity (D), and joining (J) [V(D)J] sequences of the antigen-specific T cell receptors has also been challenging due to hurdles in sequencing these large regions, particularly at the single-cell level. Here, we have expanded our previous work of combining two powerful technologies, Immudex dCODE Dextramer™ (RiO) Reagents and the BD Rhapsody™ Single-Cell Analysis System, to detect and characterize low-frequency antigen-specific T cells, including the full sequences of the V(D)J gene segments of the T cell receptors, as well as profile transcriptome and protein expression. Specifically, thousands of sorted PBMCs were multiplexed to provide high-throughput detection of individual antigen-specific CD8+ T cells in combination with the corresponding full V(D)J sequences of the T cell receptors. In addition, we simultaneously obtained gene expression data for over 400 immune-related mRNAs as well as cell phenotypes using a panel of 30 cell surface BD® AbSeq Protein Markers. Together these data can be used to define T cell phenotypes associated with T cell activation states, alongside antigen specificity of enriched CD8+ dextramer+ cells from PBMC populations. This study showcases the importance of multiomic analysis for high-resolution T cell profiling that has broader implications and utility in immuno-oncology, infectious diseases and autoimmunity.