TScan-II: A genome-scale platform for the de novo identification of CD4+ T cell epitopes

CD4+ T cells play fundamental roles in orchestrating immune responses and tissue homeostasis. However, our inability to associate peptide human leukocyte antigen class-II (HLA-II) complexes with their cognate T cell receptors (TCRs) in an unbiased manner has hampered our understanding of CD4+ T cell function and role in pathologies. Here, we introduce TScan-II, a highly sensitive genome-scale CD4+ antigen discovery platform. This platform seamlessly integrates the endogenous HLA-II antigen-processing machinery in synthetic antigen-presenting cells and TCR signaling in T cells, enabling the simultaneous screening of multiple HLAs and TCRs. Leveraging genome-scale human, virome, and epitope mutagenesis libraries, TScan-II facilitates de novo antigen discovery and deep exploration of TCR specificity. We demonstrate TScan-II’s potential for basic and translational research by identifying a non-canonical antigen for a cancer-reactive CD4+ T cell clone. Additionally, we identified two antigens for clonally expanded CD4+ T cells in Sjögren’s disease, which bind distinct HLAs and are expressed in HLA-II-positive ductal cells within affected salivary glands. [Display omitted] •TScan-II finds the cognate and cross-reactive antigens of self and viral CD4+ TCRs•Saturated mutagenesis screens facilitate the mapping of the CD4+ TCR epitope interface•CD4+ cells in Sjögren’s disease recognize self-antigens on HLA-II-positive ductal cells•TScan-II finds antigens within the non-canonical immunopeptidome for cancer TCRs TScan-II is a genome-scale platform that integrates endogenous antigen processing and T cell signaling, facilitating multiplex screens for the identification of physiologically relevant antigens recognized by CD4+ T cells. The unbiased nature of the platform allows the identification of CD4+ T cell antigens in Sjögren’s disease and pancreatic cancer tumors.