Tu105 - 10X Scrnaseq Allows Characterization of Antigen Specific T Cell Populations in Peripheral Blood and Synovium of Patients with RA

Matthew Dufort – Bioinformatics Project Leader, Center for Systems Immunology, Benaroya Research Institute; Jing Song – Staff Scientist, Center for Translational Immunology, Benaroya Research Institute; Arpit Mishra – Staff Scientist, Center for Translational Immunology, Benaroya Research Institute; Hannah DeBerg – Bioinformatics Group Manager, Center for Systems Immunology, Benaroya Research Institute; Peter Linsley – Member, Center for Systems Immunology, Benaroya Research Institute; Eddie James – Associate Member, Center for Translational Immunology, Benaroya Research Institute; Jane Buckner – President, Center for Translational Immunology, Benaroya Research Institute

Abstract Text: Single-cell analysis has emerged as a powerful tool for investigating transcriptomics and T-cell receptor(TCR) diversity. However, challenges remain in applying this technology to rare antigen specific T-cells found in peripheral blood and tissues of individuals with autoimmunity. To address this challenge, we conducted a pilot study using the 10x Chromium platform to obtain CITE-seq and TCR repertoire data from PBMC and synovial T-cells. The AIM assay was used to isolate T-cells from PBMC reactive to an RA-antigen-peptide-pool(RAA) or a viral-pool(CEFX), with DMSO as a control. Samples were hash-tagged, sorted, then applied to 10x where 40% of these cells resulted in high quality data. RAA and CEFX reactive T-cells demonstrated clonal expansion. Clonally expanded TCR found in activation cultures were also detected in unstimulated PBMC. Multi-modal analysis of the antigen reactive T-cells (using Unicell Deconvolve) showed eight clusters defined by merging gene expression and surface antibody markers. RAA T-cells were primarily assigned to Th1 and central memory CD4, while a substantial number of CEFX T-cells were assigned to the exhausted CD8 T-cells cluster. Synovial tissue with matched PBMC was available for 3 individuals. Synovial T-cells had an activated phenotype, and showed an increase in clonal expansion compared to peripheral T-cells. Synovial TCR were shared with TCR found in RAA or CEFX paired samples, indicating that synovial T-cells of the same specificity can be found in the periphery. In conclusion, our approach may provide valuable insights into the antigen specific T-cell responses and TCR dynamics associated with RA pathology.