Method for Direct Identification of Neoantigen-Specific TCRs from Tumor Specimens by High-Throughput Single-Cell Sequencing

Cancer immunotherapy approaches, such as adoptive cell transfer (ACT), proved effective against many cancer types. Yet, post-treatment analyses of ACT have suggested that efficacy may be enhanced by increasing the percentage of neoantigen-reactive T cells in the infused product. Neoantigens are new proteins that form on cancer cells when certain mutations occur in tumor DNA. Current techniques for identifying neoantigen-specific TCRs in T cell expression are labor-intensive, time-consuming and technically challenging. The ineffectiveness of these techniques is a barrier against improvement of ACT and other T cell therapies. Therefore, there is a need to develop effective techniques of identifying neoantigen-specific TCRs from tumor specimens.

National Cancer Institute (NCI) scientists developed a new method of isolating neoantigen-specific TCR sequences. The method entails the isolation of tumor-infiltrating T cells from a tumor specimen and stimulating them with neoantigen loaded dendritic cells (DCs). Isolates underwent single-cell sequencing of TCR and T-cell activation markers, IFN-γ and IL-2. This method was used to identify neoantigen-specific TCRs from three melanoma and three colorectal tumor specimens. These TCRs were then synthesized and transduced into autologous T cells, followed by testing to confirm antigen recognition. A total of 28 neoantigen-specific TCRs were identified by this process. This approach was highly reliable in identifying identical TCRs when TCR sequences were detected from two or more single cells (100%, 19 out of 19 TCRs). In summary, this single-cell approach provides an efficient process to isolate neoantigen-specific TCRs for research and clinical applications.

The NCI seeks research co-development partners and/or licensees for a method of direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing.