Abstract 4670: Evidence of neoantigen-reactive T cell response in a case of relapsing, mismatch-repair gene proficient, colorectal cancer
Authors: Mathieu Mélissa , Paradis Alexandre , Pelletier Sandy , Hébert Steven , Boutin Kevin , Audemard Éric , Mader Sylvie , Kleinman Claudia , Turcotte Simon 
Published: August 2018

Whether the endogenous T cell reactivity to antigens derived from cancer mutations, called neoantigens (neoAgs), can be exploited for immunotherapy in patients with mismatch-repair (MMR) gene proficient metastatic colorectal cancer (CRC) is largely unknown. Here, we investigated the frequency of neoAg-reactive T cells longitudinally in a patient with relapsing CRC. Using whole exome and RNA sequencing, we identified 96 single nucleotide variant (SNV), 8 frameshift and 29 insertion/deletion mutations in a liver metastasis. Co-culture assays between in vitro expanded tumor infiltrating T lymphocytes (TILs) and autologous CD40-activated B cells loaded with peptides derived from SNVs led to the identification of two CD8+ T cell clones specific for PAMA733E, and respectively 1, 4 and 2 CD4+ T cell clones specific for PABPC1G563S, PDE4DIPR685S and TRPM4A480V. T cell clonality was confirmed by TCR Sanger sequencing. We assessed the in vivo frequency of these neoAg-reactive T cell clones by TCRβ chain deep sequencing (Adaptive Biotechnologies). The dominant T cell clone, reactive to PAMA733E, represented 5.2% of TILs in the primary tumor resected in 2010, 2.2% of TILs in the colonic recurrence resected in 2011, and 3.2% of TILs in the liver metastasis resected in 2012. The neoAg-reactive T cells were also detected in the peritumoral liver, but not into the distant normal liver. Along the disease course, most reactive T cell clones were not detected in the tumor draining lymph nodes or in the peripheral blood, at an average detection capacity of 1/3680 and 1/185,495 T cells respectively. When compared to the RNAseq data from 60 other CRC liver metastases, the relatively high level of transcripts related to immune cells, antigen processing and presentation, IFN-γ responsive genes, T-cell inhibitory and stimulatory receptors, cytokines, and chemokines observed in our patient metastasis suggested that there was an ongoing spontaneous immune response intratumoraly, co-existing with many immune-suppressive molecules. Our results support that neoAg-reactive T cells can be found in non-highly mutated, MMR proficient CRC tumors, at a much higher frequency than in the peripheral blood or the draining lymph nodes. As an adjuvant strategy to prevent recurrence, it may be possible in some patients to boost the immune response against a relevant neoAg expressed in the primary tumor. At the metastatic stage, a broader array of neoAgs may be targetable.

Citation Format: Mélissa Mathieu, Alexandre Paradis, Sandy Pelletier, Steven Hébert, Kevin Boutin, Éric Audemard, Sylvie Mader, Claudia Kleinman, Simon Turcotte. Evidence of neoantigen-reactive T cell response in a case of relapsing, mismatch-repair gene proficient, colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4670.