title: Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.
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.
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Amalie Kai
authors: AK
authors: Bentzen
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors: Andrea Marion
authors: http://orcid.org/0000-0003-2928-6017
authors: AM
authors: Marquard
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Rikke
authors: R
authors: Lyngaa
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Sunil Kumar
authors: http://orcid.org/0000-0003-3382-9432
authors: SK
authors: Saini
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Sofie
authors: S
authors: Ramskov
authors: 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.
authors: Marco
authors: M
authors: Donia
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Lina
authors: L
authors: Such
authors: CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.|Cancer Immunology Unit, UCL Cancer Institute, University College London, London, UK.
authors: Andrew J S
authors: AJ
authors: Furness
authors: CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.|Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
authors: Nicholas
authors: N
authors: McGranahan
authors: CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.|Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
authors: Rachel
authors: R
authors: Rosenthal
authors: Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark.|Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
authors: Per Thor
authors: PT
authors: Straten
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors: Zoltan
authors: Z
authors: Szallasi
authors: 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.
authors: Inge Marie
authors: IM
authors: Svane
authors: CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.|Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
authors: Charles
authors: C
authors: Swanton
authors: CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.|Cancer Immunology Unit, UCL Cancer Institute, University College London, London, UK.
authors: Sergio A
authors: SA
authors: Quezada
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.|Immudex, Copenhagen, Denmark.
authors: Søren Nyboe
authors: SN
authors: Jakobsen
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors: Aron Charles
authors: http://orcid.org/0000-0003-0861-1001
authors: AC
authors: Eklund
authors: Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.
authors: Sine Reker
authors: http://orcid.org/0000-0002-5937-4344
authors: SR
authors: Hadrup
mesh_terms: D000941:Antigens / Q000235:genetics* / Q000276:immunology*; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D002478:Cells, Cultured; D058893:DNA Barcoding, Taxonomic; D005805:Genes, MHC Class I / Q000235:genetics* / Q000276:immunology; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D007118:Immunoassay / Q000379:methods*; D010455:Peptides / Q000235:genetics / Q000276:immunology; D055503:Protein Multimerization / Q000235:genetics / Q000276:immunology; D013194:Staining and Labeling / Q000379:methods
chemical_list: D000941:Antigens; D010455:Peptides