Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of death by cancer worldwide. In recent years, more attention has been directed toward the role of the gut microbiota in the initiation and progression of CRC. Several bacterial species have been associated with CRC carcinogenesis, like F. nucleatum, B. fragilis, and pathogenic E. coli strains, for which the mechanisms involved in their carcinogenic effects have partially been unraveled. However, the link between many intestinal bacteria and CRC initiation and progression remains poorly understood. Several recent studies have demonstrated T cell cross-reactivity against bacteria-derived antigens and tumor-derived antigens by molecular mimicry. Cases where this cross-reactivity resulted in enhanced anti-tumor response and improved response to immune checkpoint inhibitors have been observed. However, the notion that T cell cross-reactivity results in a suppressed anti-tumor response because of T cell exhaustion has also been proposed. Therefore, research is needed to fully understand the effects of gut microbial antigen presentation on immune reactivity during CRC development. In this project, we aim to address whether and how the presentation of gut microbial antigens may contribute to immune reactivity against colorectal tumors.
To do so, we developed a mass spectrometry-based immunopeptidomics pipeline that allows us to successfully identify both MHC I and MHC II-associated peptides from murine samples, using a TimsTOF SCP (Bruker) hyphenated with an Evosep One chromatography system. This setup allowed us to identify multiple class I and class II microbial antigens in OligoMM12 mice (elevated germ-free, gnotobiotic mice colonized with a cocktail of 12 microbial strains). Following these proof-of-concept experiments, microbial antigen presentation will be examined in healthy murine colon tissue versus colon tissue from CRC mouse models. For these studies, we can make use of a unique mouse model of invasive and microbiota-driven CRC (Zeb2IEC-Tg). Observed differences in microbial antigen presentation may offer new insights into its effects on CRC development. These data will also aid in the correct interpretation of data obtained from human CRC samples and allow the extrapolation of the observations obtained from the mouse models.