T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes

• Published in: Cell Vol. 178; no. 4; pp. 1016 - 1028.e13
• Main Authors: Kula, Tomasz, Dezfulian, Mohammad H., Wang, Charlotte I., Abdelfattah, Nouran S., Hartman, Zachary C., Wucherpfennig, Kai W., Lyerly, Herbert Kim, Elledge, Stephen J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 08-08-2019
• Subjects: antigen discovery; Antigen Presentation - immunology; Antigens, Neoplasm - genetics; Antigens, Neoplasm - immunology; Blood Donors; CD8-Positive T-Lymphocytes - metabolism; epitope discovery; epitope mutagenesis; epitope screening; Epitopes, T-Lymphocyte - immunology; Female; Gene Knockout Techniques; Genes, MHC Class I - genetics; Genes, MHC Class I - immunology; Granzymes - metabolism; HEK293 Cells; HLA Antigens - genetics; HLA Antigens - immunology; Humans; immunological screening; Neoplasm Proteins - genetics; Neoplasm Proteins - immunology; off-target screening; peptide MHC recognition; Receptors, Antigen, T-Cell - immunology; T cell epitope; T cell screening; TCR epitope; TCR-specificity; Transduction, Genetic; Transfection; TCR-specificity; peptide MHC recognition; epitope discovery; T cell screening; TCR epitope; off-target screening; T cell epitope; immunological screening; antigen discovery; epitope screening; epitope mutagenesis
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2019.07.009

T cell recognition of specific antigens mediates protection from pathogens and controls neoplasias, but can also cause autoimmunity. Our knowledge of T cell antigens and their implications for human health is limited by the technical limitations of T cell profiling technologies. Here, we present T-Scan, a high-throughput platform for identification of antigens productively recognized by T cells. T-Scan uses lentiviral delivery of antigen libraries into cells for endogenous processing and presentation on major histocompatibility complex (MHC) molecules. Target cells functionally recognized by T cells are isolated using a reporter for granzyme B activity, and the antigens mediating recognition are identified by next-generation sequencing. We show T-Scan correctly identifies cognate antigens of T cell receptors (TCRs) from viral and human genome-wide libraries. We apply T-Scan to discover new viral antigens, perform high-resolution mapping of TCR specificity, and characterize the reactivity of a tumor-derived TCR. T-Scan is a powerful approach for studying T cell responses.
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•T-Scan is a high-throughput method to identify the functional targets of CD8 T cells•We apply T-Scan to multiplex discovery of CMV antigens from bulk memory T cells•Genome-wide T-Scan finds the cognate antigen and off-targets of a self-reactive TCR
T-Scan is a cell-based, pooled screening approach for high-throughput identification of antigens productively recognized by T cells.