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Nat Biotechnol. 2016 Oct;34(10):1037-1045. doi: 10.1038/nbt.3662. Epub 2016 Aug 29.

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

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Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.
Department of Oncology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.
CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.
Cancer Immunology Unit, UCL Cancer Institute, University College London, London, UK.
Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
Immudex, Copenhagen, Denmark.


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.

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