Sensitive, Non‐Destructive Detection and Analysis of Neoantigen‐Specific T Cell Populations from Tumors and Blood

Tumor neoantigens are fragments of mutated proteins that contain the mutation, and can be presented by major histocompatibility complex molecules on tumor cells, where they are surveyed by T cells. The rapid and sensitive identification of neoantigen‐specific T cell populations from tumor tissues or blood has proven challenging. A microchip platform for the non‐destructive identification of neoantigen‐specific CD8 T cells is described. The method utilizes a library of neoantigen/MHC tetramers linked to a magnetic nanoparticle via a DNA barcode. The neoantigen‐specificity of the T cells is determined by decoding the barcode through sequential fluorescent microscopy reads. The captured T cells may be further characterized for function, or via matching the neoantigen‐specificity with the T cell receptor gene. Tumor infiltrating lymphocytes and non‐expanded peripheral blood mononuclear cells collected from melanoma patients at various time points across an anti‐PD1 therapy regimen are shown to contain overlapping neoantigen‐specific T cell populations.