T-Plex EAC

Background, rationale. Adenocarcinoma of the esophagus or esophagus/gastric junction (EAC) is an aggressive disease with median overall survival of less than a year. EAC patients undergo neoadjuvant chemo/chemoradiotherapy (NAC/R) followed by surgery, but only 20-30% of them respond. However, a fraction of patients failing NAC/R respond to adjuvant immunotherapy by immune checkpoint blockade with anti-PD-1 mAb, suggesting the ability of EAC to generate tumor antigens stimulating autologous T cell responses. Hypothesis. We posit that adjuvant immunotherapy response of EAC patients can be further improved by enhancing anti-tumor T cell responses by approaches, entailing vaccination with tumor-specific antigens and/or adoptive transfer of ex vivo expanded tumor-specific T cells. Aims. Our main objective is to provide proof of concept for the feasibility of integrating bioinformatics, biotechnology, artificial intelligence and immunology to T-Plex-Capture, an innovative multiplex platform enabling the identification of HLA-I-presented neoantigens for cancer vaccines, and the isolation of respective autologous CD8+ T cells and T cell receptors (TCRs) for adoptive cell therapy. Methods. WES and RNA-seq data from EAC samples of patients not responding to NAC/R will be utilized to in silico predict HLA-I presented mutated or frameshift tumor peptides by advanced artificial intelligence platforms. Predicted epitopes will be incorporated into recombinant HLA-I proteins and coated onto color-coded T-Plex-Capture magnetic beads, which will be applied to isolate autologous tumor-specific CD8+ T cells, followed by single-cell TCR sequencing and functional validation of cloned TCRs. Expected results and potential impact. With this innovative strategy, we intend to accelerate the presently cumbersome workflow of identification of tumor neoantigens and of specific T cells/TCRs, for their clinical application to improve the response of EAC patients to adjuvant immunotherapy.