Background Tumor-infiltrating lymphocyte (TIL) therapy can mediate tumor regression in a range of solid cancers, most notably in melanoma. However, its wider application and efficacy has been limited by the low frequency and exhausted phenotype of tumor-specific T cells in the final product. Here, we developed a personalized, neoantigen-specific TCR discovery platform that will enable engineering of multiple TCRs into autologous peripheral blood T cells. This allows for the generation of a fitter T cell product with a high frequency of tumor-reactive TCRs of defined specificity.

Methods Our platform first identifies tumor-specific mutations and TIL-derived TCR repertoires from non-viable tumor specimens using next-generation sequencing (NGS), which are subsequently recreated using synthetic biology technology. The synthesized TCR libraries are expressed in reporter T cells, whereas neoantigen libraries are engineered in autologous APCs. Following coculture of these cells, activated and non-activated T cells are separated, followed by neoantigen-specific TCR identification using NGS-based analysis.

Results We validated the high sensitivity and specificity of this platform by successfully identifying multiple TCRs and their cognate neoantigens from high tumor mutational burden (TMB) cancers including melanoma. Notably, we show that the platform is agnostic to the type of mutation and HLA class restriction. Importantly, neoantigen-specific TCRs can also be isolated from a panel of low TMB microsatellite-stable colorectal cancers, underscoring the pan-cancer potential of this approach.

Conclusions We commenced applying this approach in a clinical study in which patients will be treated with functional autologous T cells engineered with neoantigen-specific TCRs of defined specificity and composition.