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 one to several cognate peptide-MHC complexes (pMHC). Limited knowledge of TCR repertoire specificities restricts our capacity to rationally interpret this information, both diagnostically and in preclinical research. In this study, we (i) developed and validated a cost-efficient wet lab and computational pipeline to identify mouse TCRs specific to particular peptides, (ii) produced a dataset of helper T cell (Th) TCR beta chain CDR3s specific to B16 melanoma neoantigens in the I-Ab pMHCII context, available in VDJdb, and (iii) applied this dataset to track tumor-specific T-cell responses to the CTLA4 blocking immunotherapy in the orthotopic B16 melanoma model. We showed that B16-specific TCR motifs expanded in both Th and regulatory T cell (Treg) repertoires of tumor-bearing mice, with stronger expansion in the Th subset of mice treated with the 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 prominent Th clonal expansion and induces general, nontumor-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 the development and validation of immunotherapeutic and vaccination approaches.