Journal for ImmunoTherapy of Cancer (Jul 2021)

Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing

  • Steven A Rosenberg,
  • Paul F Robbins,
  • Zhili Zheng,
  • Todd D Prickett,
  • Jared J Gartner,
  • Yong-Chen Lu,
  • Frank J Lowery

DOI
https://doi.org/10.1136/jitc-2021-002595
Journal volume & issue
Vol. 9, no. 7

Abstract

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Background Recognition of neoantigens by T cells plays a major role in cancer immunotherapy. Identification of neoantigen-specific T-cell receptors (TCRs) has become a critical research tool for studying T cell-mediated responses after immunotherapy. In addition, neoantigen-specific TCRs can be used to modify the specificity of T cells for T cell-based therapies targeting tumor-specific mutations. Although several techniques have been developed to identify TCR sequences, these techniques still require a significant amount of labor, making them impractical in the clinical setting.Methods Thanks to the availability of high-throughput single-cell sequencing, we developed a new process to isolate neoantigen-specific TCR sequences. This process included the isolation of tumor-infiltrating T cells from a tumor specimen and the stimulation of T cells by neoantigen-loaded dendritic cells, followed by single-cell sequencing for TCR and T-cell activation markers, interferon-γ and interleukin-2.Results In this study, potential neoantigen-specific TCRs were isolated from three melanoma and three colorectal tumor specimens. These TCRs were then synthesized and transduced into autologous T cells, followed by testing the recognition of neoantigens. A total of 28 neoantigen-specific TCRs were identified by this process. If identical TCR sequences were detected from two or more single cells, this approach was highly reliable (100%, 19 out of 19 TCRs).Conclusion This single-cell approach provides an efficient process to isolate antigen-specific TCRs for research and clinical applications.