Cancer Immune-Interception for Lynch Syndrome

Lynch Syndrome (LS) is the most common cause of hereditary colorectal cancer (CRC), affecting >1 million Americans. LS is caused by germline mutations in the DNA mismatch repair (MMR) genes. Normal colorectal epithelial cells in LS patients become MMR deficient upon acquisition of a ‘second’ somatic hit in the alternative allele of the same MMR gene that harbors the germline mutation, thus triggering the accumulation of hundreds to thousands of base-to-base mismatches and insertion-deletion mutations (indels) in microsatellite sequences. These mutations generate frameshift peptides (FSP) that become neoantigens (neoAg) and stimulate the adaptive immune system. We have reported that LS pre-cancers are immune activated and present strikingly high levels of expression of adaptive immune genes. Therefore, LS patients constitute a well-defined and prevalent population that has the potential to benefit from immune-interception strategies to prevent CRC. We have acquired a substantial amount of genomic data from LS colorectal pre-cancers and tumors to catalog and to identify the most frequent recurrent neoAg present in these lesions. In addition, we have been studying chemopreventive strategies that could augment the immune response and observed increased activation of the resident immune cells in the colorectal mucosa upon exposure to naproxen, a non-steroidal anti-inflammatory drug (NSAID), from our biomarker analysis of our NCI-sponsored Phase Ib clinical in LS patients. Furthermore, we have performed a co-clinical trial in a humanized LS mouse model that has observed that peptide vaccination with neoAg is highly effective in preventing LS CRC with the activity that is further enhanced by its combination with naproxen, thus laying the foundations for this grant proposal. The central hypothesis of this proposal is that naproxen is an immune-modulator that activates resident immune cells in the colorectal mucosa, and these will increase the recognition of NeoAg and activation of resident T-cells eliciting tumor cell killing. To explore this hypothesis, we propose three specific aims: 1. To characterize the immune cell types that are regulated after the administration of chemopreventive naproxen and aspirin in LS patients using single-cell genomics and imaging mass cytometry within a randomized phase II clinical trial; 2. To assess the immunogenicity of candidate shared neoAg identified LS patients pre-cancers and tumors for personalized immunoprevention using tetramer bound to magnetic beads in ELISpots, Tetramer stain, and cytotoxicity assays of co-cultured patient-derived organoids and autologous CD8+ T cells; 3. To profile the T cell Receptor (TCR) of neoantigen-specific CD8+ T cell clones for tracking tumor immunogenicity in LS patients. The proposed research will significantly impact the field by developing a combination of a peptide vaccination and an NSAID for immune-interception in hereditary cancers for the first time. The proposal is highly innovative by combining a chemoprevention trial using imaging mass cytometry, single-cell genomics, and systems biology to assess trial endpoints, and using tetramers bound to magnetic beads for positive selections of clones in immunology experiments.