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

Abstract

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.

Computational Prediction and Validation of Tumor-Associated Neoantigens

“…Despite the obvious advantage of tetramer staining in identifying neoantigen-reactive T cells, this tool provides limited information on the functional status of purified T cells and their cytotoxic capacity (134). The recent development of T-scan screening technology holds promise to overcome this issue (154). Likewise, a recently developed method referred to as imPACT Isolation Technology identifies pre-existing T cell clones that recognize tumor neoantigens (155).…”

Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy

“…These studies cannot completely eliminate the risk of adverse events due to off-target reactivity in the clinic. In particular, several novel approaches to evaluating TCR specificity have been recently published, which allow the identification of mimotope peptides with minimal sequence similarity to the known index peptide, 42,43 in contrast to the X-scan which is limited to relatively conservative substitutions. In addition, the primary cell screen is performed without regard to the gene expression profile of the cell types and would benefit from a more systematic approach to selecting cells, with the aim of maximizing genomic coverage amongst the panel of cells tested.…”

Detecting Tumor Specific Antigen-Reactive T cells from Tumor Infiltrating Lymphocytes via Interaction Dependent Fucosyl-biotinylation

“…As a consequence, research time and cost are dramatically reduced compared to the aforementioned reverse immunology based pMHC tetramer approach (Arnaud et al, 2020). Significantly, once a TSA-reactive TCR is confirmed, it is possible to use other recently developed methods to identify the corresponding antigen (Gee et al, 2018;Kula et al, 2019;Li et al, 2019a).…”