Amalie Kai Bentzen; Andrea Marion Marquard; Rikke Lyngaa; Sunil Kumar Saini; Sofie Ramskov; Marco Donia; Lina Such; Andrew J. S. Furness; Nicholas McGranahan; Rachel Rosenthal; Per thor Straten; Zoltan Szallasi; Inge Marie Svane; Charles Swanton; Sergio A. Quezada; Søren Nyboe Jakobsen; Aron Charles Eklund; Sine Reker Hadrup
Nat. Biotech., 2016, 34, 1037-1045
https://doi.org/10.1038/nbt.3662

Abstract

Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10–100 distinct T-cell specificities in one sample. Here we use peptide–major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.