A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers.

Abstract

A common theme across multiple successful immunotherapies for cancer is the recognition of tumor-specific mutations (neoantigens) by Tcells. The rapid discovery of such antigen responses could lead to improved therapies through the adoptive transfer of Tcells engineered to express neoantigen-reactive Tcell receptors (TCRs). Here, through CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) and TCR-seq of non-small cell lung cancer (NSCLC) tumor-infiltrating lymphocytes (TILs), we develop a neoantigen-reactive Tcell signature based on clonotype frequency and CD39 protein and CXCL13 mRNA expression. Screening of TCRs selected by the signature allows us to identify neoantigen-reactive TCRs with a success rate of 45% for CD8+ and 66% for CD4+ Tcells. Because of the small number of samples analyzed (4 patients), generalizability remains to be tested. However, this approach can enable the quick identification of neoantigen-reactive TCRs and expedite the engineering of personalized neoantigen-reactive Tcells for therapy.