TCR-MAP: A Novel, High-throughput T Cell Antigen Discovery Platform to Identify Viral- and Self-antigen TCR Reactivities in Rheumatoid Arthritis

Abstract Text: Rheumatoid arthritis (RA) is a prevalent autoimmune disorder characterized by chronic inflammatory processes that lead to joint destruction. Immunologically, both CD4+ and CD8+ T cells are highly enriched in the synovium and contribute to the inflammation and pathology of the disease. However, the identities of the antigens that stimulate synovial T cells and how such reactivities relate to the molecular underpinnings of RA pathogenesis have remained elusive. Here, we present T Cell Receptor Mapping of Antigenic Peptides (TCR-MAP) a novel, synthetic antigen discovery platform that uses a TCR-stimulated circuit in immortalized T cells to activate sortase-mediated tagging of engineered antigen presenting cells expressing genetically encoded peptides on MHCs of interest. Tagged antigen presenting cells containing the cognate T cell epitopes can be directly purified for deconvolution by next-generation sequencing, enabling TCRs with unknown specificity to be queried against large, barcoded peptide libraries in a pooled screening context. TCR-MAP accurately captures self- or viral-reactivities with high-throughput and sensitivity for both MHC class I- (CD8+) and class II- (CD4+) restricted T cells. We have used TCR-MAP in combination with single-cell TCR profiling of T cells from patient synovial fluid to identify T cell antigens in RA. This revealed that clonally expanded synovial T cells can be highly specific or exhibit multi-antigen cross-reactivity to self- and/or viral-proteins. TCR-MAP is a powerful tool for mapping unknown TCR-antigen reactivities and further application of this technology has the potential to accelerate T cell antigen discovery efforts in the context of cancer, infectious disease, and autoimmunity.