Microsatellite stable colorectal cancer (MSS-CRC) accounts for 80-85% of all diagnosed cases of CRC, yet currently there are no specific forms of immunotherapy that can cater to this dominant disease subset. Unlike in microsatellite instable form of CRC, where checkpoint blockade is now the preferred therapy, MSS-CRC is still largely treated only with combination chemotherapies that lack strong efficacy and tumor selectivity.
We addressed this clinical need with a two-pronged approach. (1) Through detailed tumor-surface biotinylation, streptavidin retrieval and quantitative MS comparisons against normal colon, we identified novel CRC immunotherapy targets DPEP1 and SCARB1, which anti-correlate with patient survival and are indicative of early cancer based on a large patient cohort. RNAi of these targets further demonstrate direct functional involvement of these proteins in CRC progression and metastatic processes, including proliferation, migration and invasion. (2) By ribosome profiling, we identified non-canonical translated regions in MSS-CRC tumors, that may be sourced for immunopeptide presentation. By focusing on long neo-sequences that are uniquely translated in MSS-CRC, we overcome HLA restriction and established a pipeline to identify neoantigens, pulse-vaccinate patient-derived PBMCs and retrieve reactive T cells for both autologous transfer and further engineering into TCR-T immunotherapy.
Given that MSS-CRC has typically lower tumor mutational burden, our strategies target instead altered localization of wildtype proteins in the plasma membrane and translation events in tumors from wildtype long transcripts but in regions never-translated in healthy colon. Developing these further can significantly expand the treatment options for MSS-CRC, and are critical to overcome the lack of targetable mutations and the immune-cold phenotype of MSS-CRC tumors.