Circulating Neoantigen-Specific T Cells Can Be Prospectively Identified

Cancer immunotherapies are predicated on the ability of lymphocytes to recognize tumor-associated antigens, which are overexpressed in tumor cells and present at low levels in normal cells, and tumor neoantigens, which arise from tumor-specific somatic mutations. However, the inability to predict which neoantigens are the most immunogenic and to identify circulating neoantigen-specific T cells has impeded the development of neoantigen-based immunotherapy. Gros and colleagues, who recently showed that CD8⁺ tumor-infiltrating lymphocytes (TIL) that express programmed cell death 1 (PD-1) can recognize tumor-reactive T cells, investigated whether PD-1 can prospectively identify circulating neoantigen-specific lymphocytes in patients with melanoma. Analysis of matched peripheral blood samples and primary tumors revealed that although a higher proportion of CD8⁺ TILs expressed PD-1, circulating CD8⁺ lymphocytes expressed PD-1 at a low frequency. A high-throughput personalized screening strategy, which was designed to assess lymphocyte reactivity to neoepitopes presented on all HLA-restricting elements in a patient, was used to ascertain autologous T-cell reactivity to neoantigens resulting from nonsynonymous somatic mutations, which were identified by exomic and RNA sequencing of primary tumors and encoded by tandem minigenes (TMG), for four patients with melanoma. Patient-specific TMGs were expressed in dendritic cells which were co-cultured with autologous circulating lymphocytes that had been isolated from peripheral blood samples in parallel, expanded in vitro, and flow-sorted into CD8⁺, CD8⁺PD-1⁻, CD8⁺PD-1⁺, and CD8⁺PD1^hi populations. In three of the four patients, CD8⁺ lymphocytes that expressed PD-1 exhibited reactivity to tumor neoantigens. Consistent with these findings, CD8⁺PD-1⁺ lymphocytes prospectively identified a diverse neoantigen lymphocyte response and recognized autologous tumor cells. Both circulating and tumor-resident CD8⁺PD-1⁺ lymphocytes recognized similar tumor neoantigens and exhibited significantly overlapping T-cell receptor repertoires. Taken together, these results demonstrate the feasibility of identifying circulating neoantigen-specific T cells and immunogenic neoantigens and support further exploration of their use for personalized immunotherapy.

Gros A, Parkhurst MR, Tran E, Pasetto A, Robbins PF, Ilyas S, et al. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nature Medicine 2016 Feb 22 [Epub ahead of print].