Neoantigen-reactive T cells are found at low frequency in colorectal cancer liver metastases resected with curative intent
 
M. Mathieu¹, A. Paradis¹, S. Pelletier¹, S. Hébert³, K. Boutin¹, É. Audemard², S. Mader², C.L. Kleinman³ and S. Turcotte^1
1Centre hospitalier de l'Université de Montréal Research Center (CRCHUM); ²Institute for Research in Immunology and Cancer (IRIC); ³Department of Human Genetics, McGill University
 
Immunotherapy is a promising treatment for patients with metastatic colorectal cancer (CRC), a leading cause of cancer death. Efficacy of immune checkpoint inhibitors and adoptive cell transfer (ACT) has been shown to be mediated by T-cell reactivity to cancer mutated antigens i.e. neoantigen (neoAg). To gain insight into the ongoing immune response toward neoAgs, we investigated the frequency, functionality and environment of neoAg-reactive T cells found in patients with CRC liver metastases (CRCLM), a cancer with low mutational burden. Using whole exome and RNA sequencing, mutations were quantified in 5 patients with CRCLM. The mutational burden was higher for patient 243 where we identified 96 single nucleotide variants (SNV) as compared to 44, 77, 77 and 80 SNV in the others. Interestingly, in patient 243 only, CD8 and CD4 neoAg-reactive T cells were identified. Further analysis of the CRCLM RNAseq data revealed that this patient had the most immune reactive cancer characterized by, amongst other pathways, increased immune cell transcripts, expression of coinhibitory and costimulatory receptors and ligands and activation of IFN responsive genes. Indeed, by flow cytometry, TILs from patient 243 metastasis expressed higher levels of PD-1, a molecule associated with immune exhaustion but also Ag recognition. Also, the TCR repertoire from patient 243 liver metastasis was more clonal than for other patients. Globally, these results have shown that neoAg-reactive T cells are naturally found within a patient with an higher mutational burden and a pre-existing immune reactive environment. Several CD8 and CD4 TIL clones reactive to neoAg derived from SNVs in CRCLM were identified but TIL reactivity to other types of neoAgs remains to be characterized to develop effective T cell-based immunotherapy in these patients. Understanding the functional neoAg-reactive T cells biology using human tumor samples should provide key insights to select patients with refractory CRCLM who could benefit most from immunotherapy such as ACT or immunomodulation.