177P - Ubiquitous neoantigens as targets for T cell recognition in a patient with metastatic pancreatic neuroendocrine tumour

Background

Mutation-derived neoantigens, usually identified from the primary cancer, are being targeted by vaccination in clinical trials. However, clinical success in patients with extensive metastatic disease is limited, possibly due to poor neoantigen selection. Targeting ubiquitous neoantigens - present in all metastatic sites - is appealing. We investigated the presence of ubiquitous neoantigens and their T-cell recognition in a patient with treatment-naïve metastatic pancreatic neuroendocrine tumour (PNET), analysing the primary tumour and 13 synchronous nodal metastases.

Methods

Bulk RNA sequencing, whole exome sequencing and mutation calling were performed on all samples; β-chain T-cell receptor (TCR) sequencing was performed on eight metastatic sites. Mutation-associated long peptides (MUT_LPs) and predicted minimal neoepitopes (MUT_ME) were synthesized. IFN-γ ELISpot and single-cell RNA/TCR sequencing (scRNA/TCRseq) were undertaken on MUT_LPs/MEs stimulated peripheral blood mononuclear cells (PBMCs) after in vitro expansion. ScTCRseq was performed on MUT_ME-MHC class I tetramer-positive CD8 T-cells. TCR overlap was evaluated between metastatic sites, MUT_LP/ME expanded and tetramer-positive T-cells.

Results

We identified a median of 88 non-synonymous mutations (range 64-204) per site, indicating low tumour-mutation burden (TMB). Seven mutations were identified in all metastatic sites. T cell recognition was shown by ELISpot for two MUT_LPs and one MUT_ME (MUT_NPTX2). scRNAseq of MUT_NPTX2_ME/LP-expanded PBMCs showed activated CD8 T-cells; 94.8% of these cells had TCRs matching MUT_NPTX2_ME-MHC class I tetramer-positive clones. Putative MUT_NPTX2-reactive CD8 T-cells were found in all analysed metastatic sites (1.9%-7.0% of reads per site), with evidence of expansion.

Conclusions

In a low TMB setting, we found seven ubiquitous mutations. One neoantigen showed T-cell recognition, with reactive T-cells present in all analysed metastatic sites. This novel finding suggests that ubiquitous neoantigens-targeting vaccines, possibly combined with immune-checkpoint inhibitors, could be promising for patients with extensive metastatic PNET.

Legal entity responsible for the study

Prof. Christian Ottensmeier.

Funding

Whittaker Fund.

Disclosure

All authors have declared no conflicts of interest.