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T cell antigen discovery

Nature Methods volume 18, pages 873–880 (2021)Cite this article

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Abstract

T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR–peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.

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Fig. 1: Molecular basis of TCR–pMHC recognition.
Fig. 2: Schematic antigen-directed methods.
Fig. 3: Schematic TCR-directed methods.
Fig. 4: Comparison of antigen-discovery methods.

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References

  1. Davis, M. M. & Bjorkman, P. J. T-cell antigen receptor genes and T-cell recognition. Nature 334, 395–402 (1988).

    Article  CAS  PubMed  Google Scholar 

  2. La Gruta, N. L., Gras, S., Daley, S. R., Thomas, P. G. & Rossjohn, J. Understanding the drivers of MHC restriction of T cell receptors. Nat. Rev. Immunol. 18, 467–478 (2018).

    Article  PubMed  CAS  Google Scholar 

  3. Robins, H. S. et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med. 2, 47ra64 (2010).

  4. Paucek, R. D., Baltimore, D. & Li, G. The cellular immunotherapy revolution: arming the immune system for precision therapy. Trends Immunol. 40, 292–309 (2019).

    Article  CAS  PubMed  Google Scholar 

  5. Germain, R. N. T-cell development and the CD4-CD8 lineage decision. Nat. Rev. Immunol. 2, 309–322 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Godfrey, D. I., Le Nours, J., Andrews, D. M., Uldrich, A. P. & Rossjohn, J. Unconventional T cell targets for cancer immunotherapy. Immunity 48, 453–473 (2018).

    Article  CAS  PubMed  Google Scholar 

  7. Rock, K. L., Reits, E. & Neefjes, J. Present yourself! By MHC class I and MHC class II molecules. Trends Immunol. 37, 724–737 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Neefjes, J., Jongsma, M. L., Paul, P. & Bakke, O. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat. Rev. Immunol. 11, 823–836 (2011).

    Article  CAS  PubMed  Google Scholar 

  9. Reinherz, E. L. & Wang, J. H. Codification of bidentate pMHC interaction with TCR and its co-receptor. Trends Immunol. 36, 300–306 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Sewell, A. K. Why must T cells be cross-reactive? Nat. Rev. Immunol. 12, 669–677 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Nikolich-Zugich, J., Slifka, M. K. & Messaoudi, I. The many important facets of T-cell repertoire diversity. Nat. Rev. Immunol. 4, 123–132 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Mason, D. A very high level of crossreactivity is an essential feature of the T-cell receptor. Immunol. Today 19, 395–404 (1998).

    Article  CAS  PubMed  Google Scholar 

  13. Hondowicz, B. D. et al. Discovery of T cell antigens by high-throughput screening of synthetic minigene libraries. PLoS One 7, e29949 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wooldridge, L. et al. A single autoimmune T cell receptor recognizes more than a million different peptides. J. Biol. Chem. 287, 1168–1177 (2012).

    Article  CAS  PubMed  Google Scholar 

  15. Wucherpfennig, K. W. et al. Polyspecificity of T cell and B cell receptor recognition. Semin. Immunol. 19, 216–224 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Holler, P. D. et al. In vitro evolution of a T cell receptor with high affinity for peptide/MHC. Proc. Natl Acad. Sci. USA 97, 5387–5392 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Frankiw, L., Baltimore, D. & Li, G. Alternative mRNA splicing in cancer immunotherapy. Nat. Rev. Immunol. 19, 675–687 (2019).

    Article  CAS  PubMed  Google Scholar 

  18. Jurtz, V. et al. NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. J. Immunol. 199, 3360–3368 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Bassani-Sternberg, M. et al. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PLOS Comput. Biol. 13, e1005725 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Kawakami, Y. et al. Cloning of the gene coding for a shared human melanoma antigen recognized by autologous T cells infiltrating into tumor. Proc. Natl Acad. Sci. USA 91, 3515–3519 (1994). This study, along with that of van der Bruggen et al.21, constitutes pioneering T cell antigen-discovery work that identified several classic melanoma antigens.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. van der Bruggen, P. et al. A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science 254, 1643–1647 (1991).

    Article  PubMed  Google Scholar 

  22. Sahin, U. et al. Human neoplasms elicit multiple specific immune responses in the autologous host. Proc. Natl Acad. Sci. USA 92, 11810–11813 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bethune, M. T. et al. Isolation and characterization of NY-ESO-1-specific T cell receptors restricted on various MHC molecules. Proc. Natl Acad. Sci. USA 115, E10702–E10711 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Robbins, P. F. et al. A mutated beta-catenin gene encodes a melanoma-specific antigen recognized by tumor infiltrating lymphocytes. J. Exp. Med. 183, 1185–1192 (1996).

    Article  CAS  PubMed  Google Scholar 

  25. 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 

  26. McCutcheon, M. et al. A sensitive ELISPOT assay to detect low-frequency human T lymphocytes. J. Immunol. Methods 210, 149–166 (1997).

    Article  CAS  PubMed  Google Scholar 

  27. Ogunshola, F. et al. Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants. Nat. Commun. 9, 5023 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Koh, S. et al. A practical approach to immunotherapy of hepatocellular carcinoma using T cells redirected against hepatitis B virus. Mol. Ther. Nucleic Acids 2, e114 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Joglekar, A. V. et al. T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable. Proc. Natl Acad. Sci. USA 115, 1877–1882 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Bertoletti, A. et al. Cytotoxic T lymphocyte response to a wild type hepatitis B virus epitope in patients chronically infected by variant viruses carrying substitutions within the epitope. J. Exp. Med. 180, 933–943 (1994).

    Article  CAS  PubMed  Google Scholar 

  31. Mottez, E. et al. A single-chain murine class I major transplantation antigen. Eur. J. Immunol. 21, 467–471 (1991).

    Article  CAS  PubMed  Google Scholar 

  32. Uger, R. A., Barber, B. H. & Creating, C. T. L. targets with epitope-linked beta 2-microglobulin constructs. J. Immunol. 160, 1598–1605 (1998).

    CAS  PubMed  Google Scholar 

  33. Yu, Y. Y., Netuschil, N., Lybarger, L., Connolly, J. M. & Hansen, T. H. Cutting edge: single-chain trimers of MHC class I molecules form stable structures that potently stimulate antigen-specific T cells and B cells. J. Immunol. 168, 3145–3149 (2002).

    Article  CAS  PubMed  Google Scholar 

  34. Kim, S. et al. Single-chain HLA-A2 MHC trimers that incorporate an immunodominant peptide elicit protective T cell immunity against lethal West Nile virus infection. J. Immunol. 184, 4423–4430 (2010).

    Article  CAS  PubMed  Google Scholar 

  35. Linnemann, C. et al. High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma. Nat. Med. 21, 81–85 (2015).

    Article  CAS  PubMed  Google Scholar 

  36. Altman, J. D. et al. Phenotypic analysis of antigen-specific T lymphocytes. Science 274, 94–96 (1996). This study described the use of pMHC tetramers for identification and characterization of antigen-specific T lymphocytes.

    Article  CAS  PubMed  Google Scholar 

  37. Dolton, G. et al. More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers. Immunology 146, 11–22 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Klenerman, P., Cerundolo, V. & Dunbar, P. R. Tracking T cells with tetramers: new tales from new tools. Nat. Rev. Immunol. 2, 263–272 (2002).

    Article  CAS  PubMed  Google Scholar 

  39. Wooldridge, L. et al. Tricks with tetramers: how to get the most from multimeric peptide-MHC. Immunology 126, 147–164 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Chen, H. et al. TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection. Nat. Immunol. 13, 691–700 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Yang, J. D. et al. Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages. PLoS Pathog. 14, e1007060 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Toebes, M. et al. Design and use of conditional MHC class I ligands. Nat. Med. 12, 246–251 (2006).

    Article  CAS  PubMed  Google Scholar 

  43. Bakker, A. H. et al. Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Proc. Natl Acad. Sci. USA 105, 3825–3830 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Saini, S. K. et al. Dipeptides catalyze rapid peptide exchange on MHC class I molecules. Proc. Natl Acad. Sci. USA 112, 202–207 (2015).

    Article  CAS  PubMed  Google Scholar 

  45. Bethune, M. T., Comin-Anduix, B., Hwang Fu, Y. H., Ribas, A. & Baltimore, D. Preparation of peptide-MHC and T-cell receptor dextramers by biotinylated dextran doping. Biotechniques 62, 123–130 (2017).

  46. Luimstra, J. J. et al. A flexible MHC class I multimer loading system for large-scale detection of antigen-specific T cells. J. Exp. Med. 215, 1493–1504 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hadrup, S. R. et al. Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers. Nat. Methods 6, 520–526 (2009).

    Article  CAS  PubMed  Google Scholar 

  48. Newell, E. W., Klein, L. O., Yu, W. & Davis, M. M. Simultaneous detection of many T-cell specificities using combinatorial tetramer staining. Nat. Methods 6, 497–499 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. van Rooij, N. et al. Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J. Clin. Oncol. 31, e439–e442 (2013).

    Article  PubMed  Google Scholar 

  50. Newell, E. W., Sigal, N., Bendall, S. C., Nolan, G. P. & Davis, M. M. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 36, 142–152 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ornatsky, O., Baranov, V. I., Bandura, D. R., Tanner, S. D. & Dick, J. Multiple cellular antigen detection by ICP-MS. J. Immunol. Methods 308, 68–76 (2006).

    Article  CAS  PubMed  Google Scholar 

  52. Bendall, S. C. et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332, 687–696 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Newell, E. W. et al. Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. Nat. Biotechnol. 31, 623–629 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Fehlings, M. et al. Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells. Nat. Commun. 8, 562 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Rammensee, H. G., Falk, K. & Rötzschke, O. Peptides naturally presented by MHC class I molecules. Annu. Rev. Immunol. 11, 213–244 (1993).

    Article  CAS  PubMed  Google Scholar 

  56. Robins, H. S. et al. Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood 114, 4099–4107 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Stevanović, S. & Schild, H. Quantitative aspects of T cell activation—peptide generation and editing by MHC class I molecules. Semin. Immunol. 11, 375–384 (1999).

    Article  PubMed  CAS  Google Scholar 

  58. Bentzen, A. K. et al. Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes. Nat. Biotechnol. 34, 1037–1045 (2016). This work, along with the study by Zhang et al.62, described DNA-barcode-based pMHC multimer technology to access peptide specificity and decipher TCR αβ TCR sequences in large scale.

    Article  CAS  PubMed  Google Scholar 

  59. Saini, S. K. et al. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. Semin. Immunol. 4, eaau9039 (2019).

    CAS  Google Scholar 

  60. Bentzen, A. K. et al. T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes. Nat. Biotechnol. 36, 1191–1196 (2018).

    Article  CAS  Google Scholar 

  61. Pedersen, N. W. et al. CD8+ T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens. Nat. Commun. 10, 837 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  62. Zhang, S. Q. et al. High-throughput determination of the antigen specificities of T cell receptors in single cells. Nat. Biotechnol. 36, 1156–1159 (2018).

    Article  CAS  Google Scholar 

  63. Xu, Q., Schlabach, M. R., Hannon, G. J. & Elledge, S. J. Design of 240,000 orthogonal 25mer DNA barcode probes. Proc. Natl Acad. Sci. USA 106, 2289–2294 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Peng, S. et al. Sensitive detection and analysis of neoantigen-specific T cell populations from tumors and Blood. Cell Rep 28, 2728–2738 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Segaliny, A. I. et al. Functional TCR T cell screening using single-cell droplet microfluidics. Lab Chip 18, 3733–3749 (2018). This study utilized droplet microfluidics technology for functional screening and real-time monitoring of single TCR T cell activation upon recognition of target tumor cells.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Varadarajan, N. et al. Rapid, efficient functional characterization and recovery of HIV-specific human CD8+ T cells using microengraving. Proc. Natl Acad. Sci. USA 109, 3885–3890 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Ng, A. H. C. et al. MATE-Seq: microfluidic antigen-TCR engagement sequencing. Lab Chip 19, 3011–3021 (2019).

    Article  CAS  PubMed  Google Scholar 

  68. Hemmer, B. et al. Identification of high potency microbial and self ligands for a human autoreactive class II-restricted T cell clone. J. Exp. Med. 185, 1651–1659 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Gavin, M. A., Dere, B., Grandea, A. G. III, Hogquist, K. A. & Bevan, M. J. Major histocompatibility complex class I allele-specific peptide libraries: identification of peptides that mimic an H-Y T cell epitope. Eur. J. Immunol. 24, 2124–2133 (1994).

    Article  CAS  PubMed  Google Scholar 

  70. Pinilla, C. et al. Combinatorial peptide libraries as an alternative approach to the identification of ligands for tumor-reactive cytolytic T lymphocytes. Cancer Res. 61, 5153–5160 (2001).

    CAS  PubMed  Google Scholar 

  71. Gavin, M. A. & Bevan, M. J. Major histocompatibility complex allele-specific peptide libraries and identification of T-cell mimotopes. Methods Mol. Biol. 87, 235–248 (1998).

    CAS  PubMed  Google Scholar 

  72. Wilson, D. B. et al. Immunogenicity. I. Use of peptide libraries to identify epitopes that activate clonotypic CD4+ T cells and induce T cell responses to native peptide ligands. J. Immunol. 163, 6424–6434 (1999).

    CAS  PubMed  Google Scholar 

  73. Hiemstra, H. S. et al. The identification of CD4+ T cell epitopes with dedicated synthetic peptide libraries. Proc. Natl Acad. Sci. USA 94, 10313–10318 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Rubio-Godoy, V. et al. Combinatorial peptide library-based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity. Eur. J. Immunol. 32, 2292–2299 (2002).

    Article  CAS  PubMed  Google Scholar 

  75. Sherev, T., Wiesmüller, K. H. & Walden, P. Mimotopes of tumor-associated T-cell epitopes for cancer vaccines determined with combinatorial peptide libraries. Mol. Biotechnol. 25, 53–61 (2003).

    Article  CAS  PubMed  Google Scholar 

  76. Linnemann, T. et al. Mimotopes for tumor-specific T lymphocytes in human cancer determined with combinatorial peptide libraries. Eur. J. Immunol. 31, 156–165 (2001).

    Article  CAS  PubMed  Google Scholar 

  77. Nino-Vasquez, J. J. et al. A powerful combination: the use of positional scanning libraries and biometrical analysis to identify cross-reactive T cell epitopes. Mol. Immunol. 40, 1063–1074 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Barber, J. S. et al. Peptide library-based evaluation of T-cell receptor breadth detects defects in global and regulatory activation in human immunologic diseases. Proc. Natl Acad. Sci. USA 110, 8164–8169 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Ernst, W. et al. Baculovirus surface display: construction and screening of a eukaryotic epitope library. Nucleic Acids Res. 26, 1718–1723 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kozono, H., White, J., Clements, J., Marrack, P. & Kappler, J. Production of soluble MHC class II proteins with covalently bound single peptides. Nature 369, 151–154 (1994).

    Article  CAS  PubMed  Google Scholar 

  81. Szardenings, M. Phage display of random peptide libraries: applications, limits, and potential. J. Recept. Signal Transduct. Res. 23, 307–349 (2003).

    Article  CAS  PubMed  Google Scholar 

  82. Crawford, F., Huseby, E., White, J., Marrack, P. & Kappler, J. W. Mimotopes for alloreactive and conventional T cells in a peptide-MHC display library. PLoS Biol. 2, E90 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  83. Wang, Y. et al. Using a baculovirus display library to identify MHC class I mimotopes. Proc. Natl Acad. Sci. USA 102, 2476–2481 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Crawford, F. et al. Use of baculovirus MHC/peptide display libraries to characterize T-cell receptor ligands. Immunol. Rev. 210, 156–170 (2006).

    Article  CAS  PubMed  Google Scholar 

  85. Wen, F., Sethi, D. K., Wucherpfennig, K. W. & Zhao, H. Cell surface display of functional human MHC class II proteins: yeast display versus insect cell display. Protein Eng. Des. Sel. 24, 701–709 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Birnbaum, M. E., Dong, S. & Garcia, K. C. Diversity-oriented approaches for interrogating T-cell receptor repertoire, ligand recognition, and function. Immunol. Rev. 250, 82–101 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Brophy, S. E., Holler, P. D. & Kranz, D. M. A yeast display system for engineering functional peptide-MHC complexes. J. Immunol. Methods 272, 235–246 (2003).

    Article  CAS  PubMed  Google Scholar 

  88. Boder, E. T. & Wittrup, K. D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553–557 (1997). This report describes yeast display of combinatorial polypeptide libraries.

    Article  CAS  PubMed  Google Scholar 

  89. Kieke, M. C., Cho, B. K., Boder, E. T., Kranz, D. M. & Wittrup, K. D. Isolation of anti-T cell receptor scFv mutants by yeast surface display. Protein Eng. 10, 1303–1310 (1997).

    Article  CAS  PubMed  Google Scholar 

  90. Boder, E. T., Bill, J. R., Nields, A. W., Marrack, P. C. & Kappler, J. W. Yeast surface display of a noncovalent MHC class II heterodimer complexed with antigenic peptide. Biotechnol. Bioeng. 92, 485–491 (2005).

    Article  CAS  PubMed  Google Scholar 

  91. Wen, F., Esteban, O. & Zhao, H. Rapid identification of CD4+ T-cell epitopes using yeast displaying pathogen-derived peptide library. J. Immunol. Methods 336, 37–44 (2008).

    Article  CAS  PubMed  Google Scholar 

  92. Wen, F. & Zhao, H. Construction and screening of an antigen-derived peptide library displayed on yeast cell surface for CD4+ T cell epitope identification. Methods Mol. Biol. 1061, 245–264 (2013).

    Article  CAS  PubMed  Google Scholar 

  93. Adams, J. J. et al. T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Immunity 35, 681–693 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Gee, M. H. et al. Antigen identification for orphan T cell receptors expressed on tumor-infiltrating lymphocytes. Cell 172, 549–563 (2018).

    Article  CAS  PubMed  Google Scholar 

  95. Birnbaum, M. E. et al. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157, 1073–1087 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Starwalt, S. E., Masteller, E. L., Bluestone, J. A. & Kranz, D. M. Directed evolution of a single-chain class II MHC product by yeast display. Protein Eng. 16, 147–156 (2003).

    Article  CAS  PubMed  Google Scholar 

  97. Davis, M. M. & Boyd, S. D. Recent progress in the analysis of αβT cell and B cell receptor repertoires. Curr. Opin. Immunol. 59, 109–114 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Joglekar, A. V. et al. T cell antigen discovery via signaling and antigen-presenting bifunctional receptors. Nat. Methods 16, 191–198 (2019). This study, along with Kisielow et al.99, Kula et al.100, Li et al.101 and Sharma et al.102, described cell-based epitope discovery methods.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Kisielow, J., Obermair, F.-J. & Kopf, M. Deciphering CD4+ T cell specificity using novel MHC-TCR chimeric receptors. Nat. Immunol. 20, 652–662 (2019).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Li, G. et al. T cell antigen discovery via trogocytosis. Nat. Methods 16, 183–190 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Sharma, G., Rive, C. M. & Holt, R. A. Rapid selection and identification of functional CD8+ T cell epitopes from large peptide-coding libraries. Nat. Commun. 10, 4553 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Joly, E. & Hudrisier, D. What is trogocytosis and what is its purpose? Nat. Immunol. 4, 815 (2003).

    Article  CAS  PubMed  Google Scholar 

  104. Emerson, R. O. et al. Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat. Genet. 49, 659–665 (2017).

    Article  CAS  PubMed  Google Scholar 

  105. DeWitt, W. S. III et al. Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. Elife 7, e38358 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  106. Huth, A., Liang, X., Krebs, S., Blum, H. & Moosmann, A. Antigen-specific TCR signatures of cytomegalovirus infection. J. Immunol. 202, 979–990 (2019).

    Article  CAS  PubMed  Google Scholar 

  107. Dash, P. et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 547, 89–93 (2017). This study, along with Glanville et al.108, reported major advances in predicting epitope specificity based on TCR sequence.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Glanville, J. et al. Identifying specificity groups in the T cell receptor repertoire. Nature 547, 94–98 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Lanzarotti, E., Marcatili, P. & Nielsen, M. T-cell receptor cognate target prediction based on paired α and β chain sequence and structural CDR loop similarities. Front. Immunol. 10, 2080 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Ostmeyer, J., Christley, S., Toby, I. T. & Cowell, L. G. Biophysicochemical motifs in T-cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocyte and adjacent healthy tissue. Cancer Res. 79, 1671–1680 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Li, B. et al. Investigation of antigen-specific T cell receptor clusters in human cancers. Clin. Cancer Res. 26, 1359–1371 (2019).

    PubMed  Google Scholar 

  112. Carter, J. A. et al. Single T cell sequencing demonstrates the functional role of αβ TCR pairing in cell lineage and antigen specificity. Front. Immunol. 10, 1516 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Singh, N. K. et al. Emerging concepts in TCR specificity: rationalizing and (maybe) predicting outcomes. J. Immunol. 199, 2203–2213 (2017).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank K. Ford and K. Rankin for comments and suggestions on the manuscript. The figures were created with BioRender.com. This work was supported by the National Natural Science Foundation (81972875), the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences (No. 2019PT310028) and The CAMS Initiative for Innovative Medicine (2016-I2M-1-005).

Author information

Authors and Affiliations

  1. Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

    Alok V. Joglekar

  2. Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

    Alok V. Joglekar

  3. Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

    Alok V. Joglekar

  4. Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

    Guideng Li

  5. Suzhou Institute of Systems Medicine, Suzhou, China

    Guideng Li

  6. Key Laboratory of Synthetic Biology Regulatory Element, Chinese Academy of Medical Sciences, Beijing, China

    Guideng Li

Authors
  1. Alok V. Joglekar
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  2. Guideng Li
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Correspondence to Alok V. Joglekar or Guideng Li.

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Joglekar, A.V., Li, G. T cell antigen discovery. Nat Methods 18, 873–880 (2021). https://doi.org/10.1038/s41592-020-0867-z

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