Next-generation detection of antigen-responsive T cells using DNA barcode-labeled MHC-I 1 multimers

27 The identification of specific peptides recognized by T cells is important for understanding and 28 treating immune-related diseases. Current cytometry-based approaches are limited to the 29 simultaneous screening of T cell reactivity towards 10–100 distinct peptide specificities in a single 30 sample. We present a novel technology validated to screen for T cell recognition of multiple 31 (>1000) peptide specificities in a single sample using peptide-MHC multimers labeled with 32 individual DNA barcodes. Among MHC multimer-binding T cells the relative frequency of 33 sequenced DNA barcodes originating from a given peptide-MHC motif is related to the size of the 34 antigen-responsive T cell population. We demonstrate the application of DNA barcode-labeled 35 MHC multimers for the detection of rare T cell populations of both virusand cancer-restricted 36 origins in various tissues. This technology enables true high-throughput detection of antigen37 responsive T cells and opens the possibility of genome-wide immune assessments on a personalized 38 basis. 39