Capturing and tracking clonal T cell response to cancer neoantigens

In humans and mice, the T cell receptor (TCR) of each effector/memory T cell clone recognizes from one to several cognate peptide-MHC complexes (pMHC). Limited knowledge on TCR repertoire specificities restricts our capacity to rationally interpret this information, both diagnostically and in preclinical research. Here we 1) developed and validated a cost-efficient wet lab and computational pipeline to identify mouse TCRs specific to particular peptides, 2) produced a dataset of helper T cells (Th) TCRβ CDR3s specific to B16 melanoma neoantigens in the I-Ab pMHCII context, available in VDJdb, and 3) applied this dataset to track tumor-specific T cell response to the CTLA4 blocking immunotherapy on orthotopic B16 melanoma model. We showed that B16-specific TCR motifs expanded in both Th and Treg repertoires of tumor-bearing mice, with stronger expansion in the Th subset of mice treated with CTLA4 blocking antibody. The response was stochastic across individual mice with respect to the specific TCR motifs and target peptides involved - each mouse displayed a unique response pattern, likely reflecting the natural diversity of molecular pathways underlying antitumor immunity. We also showed that CTLA4 blockade promotes Th clonal expansion and induces general, non-tumor-specific Th-to-Treg plasticity. Altogether, we provide a universal pipeline for the investigation of mouse T cell responses at the antigen-specific level, facilitating development and validation of immunotherapeutic and vaccination approaches.