PMID- 33483338 OWN - NLM STAT- MEDLINE DCOM- 20220221 LR - 20220221 IS - 2470-9468 (Electronic) IS - 2470-9468 (Linking) VI - 6 IP - 55 DP - 2021 Jan 22 TI - Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells. LID - 10.1126/sciimmunol.abf4001 [doi] LID - eabf4001 AB - A major limitation to understanding the associations of human leukocyte antigen (HLA) and CD8(+) and CD4(+) T cell receptor (TCR) genes with disease pathophysiology is the technological barrier of identifying which HLA molecules, epitopes, and TCRs form functional complexes. Here, we present a high-throughput epitope identification system that combines capture of T cell-secreted cytokines by barcoded antigen-presenting cells (APCs), cell sorting, and next-generation sequencing to identify class I- and class II-restricted epitopes starting from highly complex peptide-encoding oligonucleotide pools. We engineered APCs to express anti-cytokine antibodies, a library of DNA-encoded peptides, and multiple HLA class I or II molecules. We demonstrate that these engineered APCs link T cell activation-dependent cytokines with the DNA that encodes the presented peptide. We validated this technology by showing that we could select known targets of viral epitope-, neoepitope-, and autoimmune epitope-specific TCRs, starting from mixtures of peptide-encoding oligonucleotides. Then, starting from 10 TCRbeta sequences that are found commonly in humans but lack known targets, we identified seven CD8(+) or CD4(+) TCR-targeted epitopes encoded by the human cytomegalovirus (CMV) genome. These included known epitopes, as well as a class I and a class II CMV epitope that have not been previously described. Thus, our cytokine capture-based assay makes use of a signal secreted by both CD8(+) and CD4(+) T cells and allows pooled screening of thousands of encoded peptides to enable epitope discovery for orphan TCRs. Our technology may enable identification of HLA-epitope-TCR complexes relevant to disease control, etiology, or treatment. CI - Copyright (c) 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. FAU - Lee, Mark N AU - Lee MN AUID- ORCID: 0000-0002-9576-9589 AD - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. mark_lee@post.harvard.edu matthew_meyerson@dfci.harvard.edu. AD - Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. AD - Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. FAU - Meyerson, Matthew AU - Meyerson M AUID- ORCID: 0000-0002-9133-8108 AD - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. mark_lee@post.harvard.edu matthew_meyerson@dfci.harvard.edu. AD - Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. AD - Departments of Genetics and Medicine, Harvard Medical School, Boston, MA 02115, USA. LA - eng GR - R35 CA197568/CA/NCI NIH HHS/United States GR - T32 HL007627/HL/NHLBI NIH HHS/United States GR - T32 HL066987/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Sci Immunol JT - Science immunology JID - 101688624 RN - 0 (Cytokines) RN - 0 (Epitopes, T-Lymphocyte) RN - 0 (Histocompatibility Antigens Class I) RN - 0 (Histocompatibility Antigens Class II) RN - 0 (Peptide Library) RN - 0 (Receptors, Antigen, T-Cell) SB - IM MH - Antigen Presentation MH - Antigen-Presenting Cells/*immunology/metabolism MH - CD4-Positive T-Lymphocytes/immunology/metabolism MH - CD8-Positive T-Lymphocytes/immunology/metabolism MH - Cell Engineering MH - Cytokines/metabolism MH - Epitope Mapping/*methods MH - Epitopes, T-Lymphocyte/*immunology/metabolism MH - HEK293 Cells MH - HeLa Cells MH - High-Throughput Screening Assays MH - Histocompatibility Antigens Class I/immunology/metabolism MH - Histocompatibility Antigens Class II/immunology/metabolism MH - Humans MH - Jurkat Cells MH - Peptide Library MH - Receptors, Antigen, T-Cell/immunology/*metabolism PMC - PMC8320540 MID - NIHMS1712920 EDAT- 2021/01/24 06:00 MHDA- 2022/02/22 06:00 PMCR- 2021/07/29 CRDT- 2021/01/23 05:33 PHST- 2020/10/23 00:00 [received] PHST- 2020/12/17 00:00 [accepted] PHST- 2021/01/23 05:33 [entrez] PHST- 2021/01/24 06:00 [pubmed] PHST- 2022/02/22 06:00 [medline] PHST- 2021/07/29 00:00 [pmc-release] AID - 6/55/eabf4001 [pii] AID - 10.1126/sciimmunol.abf4001 [doi] PST - ppublish SO - Sci Immunol. 2021 Jan 22;6(55):eabf4001. doi: 10.1126/sciimmunol.abf4001.