The neoantigen and associated tumour microenvironment in long-term survivors with oesophageal adenocarcinoma

Background Oesophageal adenocarcinoma (OAC) is a highly mutated cancer with poor survival. While outcomes are improving, long-term survival remains elusive for the majority of patients. Immunotherapy in combination with chemotherapy has shown benefit but is effective in only a subset of patients, highlighting the lack of reliable genomic biomarkers for response and survival. Effective anti-tumour immune responses, including those targeting neoantigens, are critical for durable outcomes. However, their role in long-term OAC survivors remains poorly understood. Methods Whole-genome, whole-exome, and RNA sequencing data was used to identify (expressed) putative neoantigens from two independent OAC cohorts. We combined data from the Extended-DOCTOR (ExtDOC; n=149) and the TCGA ESCA (n=88) cohort to profile the neoantigen landscape in OAC. 95 patients of the ExtDOC cohort were enrolled in the DOCTOR trial, sponsored by the GI Cancer Trials. Selected putative neoantigens from 14 patients underwent in vitro validation using HLA-matched healthy donor and patient-derived PBMCs. Results We identified a median of 23 neoantigens per tumour sample which were mostly 9- and 10-mers predicted to bind to HLA-A molecules. Low stromal and immune exclusion scores as well as high-quality neoantigens with high expressed differential agretopicity index (DAI), a measure of immunogenicity, were linked to good survival outcomes. We observed intra-tumour heterogeneity and found immunogenic putative neoantigens for 12/14 patients. The tumour environment (TME) revealed three immune clusters which were associated with patient outcomes. Conclusions We showed that OAC is characterised by a complex and largely immunosuppressive TME. In our cohort, patients with an immune-enriched TME had more favourable outcomes, including higher response rates, lower disease recurrence and longer survival. This might be linked to the presence of high-quality neoantigens. Together, these findings provide a rationale for the development of tailored, immune-informed treatment strategies in OAC.