Rapid selection and identification of functional CD8+ T cell epitopes from large peptide-coding libraries

Nat Commun. 2019 Oct 7;10(1):4553. doi: 10.1038/s41467-019-12444-7.


Cytotoxic CD8+ T cells recognize and eliminate infected or malignant cells that present peptide epitopes derived from intracellularly processed antigens on their surface. However, comprehensive profiling of specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T cell response has been challenging. Here, we report a method for deep and unbiased T cell epitope profiling, using in vitro co-culture of CD8+ T cells together with target cells transduced with high-complexity, epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T cells in co-culture are isolated prior to apoptosis by fluorescence-activated cell sorting, and characterized by sequencing the encoded minigenes. We then validate this highly parallelized method using known murine T cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries. Our data thus suggest that this epitope profiling method allows unambiguous and sensitive identification of naturally processed and MHC-presented peptide epitopes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CD8-Positive T-Lymphocytes / immunology*
  • Cell Line, Tumor
  • Cells, Cultured
  • Coculture Techniques
  • Cytotoxicity, Immunologic / immunology
  • Epitopes, T-Lymphocyte / immunology*
  • HEK293 Cells
  • Humans
  • Male
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Peptide Library*
  • T-Lymphocytes, Cytotoxic / immunology*


  • Epitopes, T-Lymphocyte
  • Peptide Library