Taylor, P. M. & Askonas, B. A. Influenza nucleoprotein-specific cytotoxic T cell clones are protective in vivo. Immunology 58, 417–420 (1986).

CAS  PubMed  PubMed Central  Google Scholar 

Tarke, A. et al. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep. Med. 2, 100204 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Smith, C. J. et al. Stochastic expansions maintain the clonal stability of CD8+ T cell populations undergoing memory inflation driven by murine cytomegalovirus. J. Immunol. 204, 112–121 (2020).

Article  CAS  PubMed  Google Scholar 

Oliveira, G. et al. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma. Nature 596, 119–125 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lowery, F. J. et al. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science 375, 877–884 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Caushi, J. X. et al. Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. Nature 596, 126–132 (2021).

Zheng, C. et al. Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers. Cancer Cell 40, 410–423.e7 (2022).

Article  PubMed  Google Scholar 

Wong, F. S. et al. Identification of an MHC class I-restricted autoantigen in type 1 diabetes by screening an organ-specific cDNA library. Nat. Med. 5, 1026–1031 (1999).

Article  CAS  PubMed  Google Scholar 

Nakayama, M. et al. Prime role for an insulin epitope in the development of type 1 diabetes. Nature 435, 220–223 (2005).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Varrin-Doyer, M. et al. MOG transmembrane and cytoplasmic domains contain highly stimulatory T cell epitopes in MS. Neurol. Neuroimmunol. Neuroinflamm. 1, e20 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Kumar, B. V., Connors, T. J. & Farber, D. L. Human T cell development, localization, and function throughout life. Immunity 48, 202–213 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, S. et al. RNase H-dependent PCR-enabled T cell receptor sequencing for highly specific and efficient targeted sequencing of T cell receptor mRNA for single-cell and repertoire analysis. Nat. Protoc. 14, 2571–2594 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Simone, M., Rossetti, G. & Pagani, M. Single cell T cell receptor sequencing: techniques and future challenges. Front. Immunol. https://doi.org/10.3389/fimmu.2018.01638 (2018).

10x Genomics. Chromium next GEM single cell V(D)J reagent kits v1.1 with feature barcode technology for cell surface protein. https://www.10xgenomics.com/support/single-cell-immune-profiling/documentation/steps/library-prep/chromium-single-cell-v-d-j-reagent-kits-user-guide-v-1-1-chemistry-with-feature-barcoding-technology-for-cell-surface-protein (2021).

Lee, M. N. & Meyerson, M. Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells. Sci. Immunol. 6, 1–15 (2021).

Article  Google Scholar 

Kula, T. et al. T-Scan: a genome-wide method for the systematic discovery of T cell epitopes. Cell 178, 1016–1028.e13 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lechner, F. et al. Analysis of successful immune responses in persons infected with hepatitis C virus. J. Exp. Med. 191, 1499–1512 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wilson, J. D. K. et al. Direct visualization of HIV-1-specific cytotoxic T lymphocytes during primary infection. Aids 14, 225–233 (2000).

Article  CAS  PubMed  Google Scholar 

Callan, M. F. C. et al. Direct visualization of antigen-specific CD8+T cells during the primary immune response to Epstein–Barr virus in vivo. J. Exp. Med. 187, 1395–1402 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fahad, A. S. et al. Cell activation-based screening of natively paired human T cell receptor repertoires. Sci. Rep. 13, 8011 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oliveira, G. et al. Landscape of helper and regulatory antitumour CD4+ T cells in melanoma. Nature 605, 532–538 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu, Z. et al. A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. Blood 132, 1911–1921 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keskin, D. B. et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature 565, 234–239 (2019).

Article  CAS  PubMed  Google Scholar 

Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

Article  CAS  PubMed  Google Scholar 

Wolfl, M. et al. Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities. Blood 110, 201–210 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duong, C. P. M. et al. Engineering T cell function using chimeric antigen receptors identified using a DNA library approach. PLoS ONE 8, e63037 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ziegler, S. F., Ramsdell, F. & Alderson, M. R. The activation antigen CD69. Stem Cells 12, 456–465 (1994).

Article  CAS  PubMed  Google Scholar 

Heemskerk, M. H. M. et al. Redirection of antileukemic reactivity of peripheral T lymphocytes using genetransfer of minor histocompatibility antigen HA-2-specific T cell receptor complexes expressing a conserved alpha joining region. Blood 102, 3530–3540 (2003).

Article  CAS  PubMed  Google Scholar 

Rosskopf, S. et al. A Jurkat 76 based triple parameter reporter system to evaluate TCR functions and adoptive T cell strategies. Oncotarget 9, 17608–17619 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Grailer, J. et al. A novel cell-based luciferase reporter platform for the development and characterization of T cell redirecting therapies and vaccine development. J. Immunother. 46, 96–106 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bialer, G., Horovitz-Fried, M., Ya’acobi, S., Morgan, R. A. & Cohen, C. J. Selected murine residues endow human TCR with enhanced tumor recognition. J. Immunol. 184, 6232–6241 (2010).

Article  CAS  PubMed  Google Scholar 

Cohen, C. J., Zhao, Y., Zheng, Z., Rosenberg, S. A. & Morgan, R. A. Enhanced antitumor activity of murine–human hybrid T cell receptor (TCR) in human lymphocytes is associated with improved pairing and TCR/CD3 stability. Cancer Res. 66, 8878–8886 (2006).

Article  CAS  PubMed