Dissecting microbiome–host crosstalk in epithelial, stromal, and immune compartments of primary and metastatic colorectal cancer

The gut microbiome has co-evolved with multicellular organisms since their earliest emergence and is now recognized as a key modulator of health and disease, including in colorectal cancer (CRC). CRC is the third most prevalent cancer globally and presents a major health burden, particularly in its metastatic stages. This thesis investigates the role of the gut microbiome in CRC pathogenesis, with a focus on its interactions within the tumor microenvironment (TME), specifically the epithelial, immune, and stromal compartments. Within the epithelial compartment, the most well studied interface for host–microbiome interactions, we study two CRC-associated bacteria, Gemella morbillorum (Gm) and Fusobacterium nucleatum (Fn), as critical contributors. In Paper I, Gm is characterized as an invasive pathogen capable of inducing DNA damage in CRC cells. In Paper II, we show that Fn promotes CRC stemness and invasiveness through the secretion of formate, highlighting a previously underexplored aspect of host–microbiome crosstalk via the secretion of metabolites. Both bacteria also modulate the immune compartment. Gm suppresses group 3 innate lymphoid cells (ILC3s) by downregulating IL-22 secretion, leading to reduced gut barrier integrity (Paper I). Fn, through formate secretion, promotes Th17 cell proliferation and promotes a pro-inflammatory environment (Paper II). These immunomodulatory effects in turn further influence the epithelial barrier, particularly in the case of Gm. In Paper III, we explore the less well studied stromal compartment, focusing on the interaction between Fn and cancer-associated fibroblasts (CAFs). We find that Fn drives CAFs toward a pro-inflammatory iCAF phenotype, in turn enhancing CRC epithelial cell migration and invasion. While Papers I–III focus on primary tumor–microbiome interactions, metastasis represents the critical clinical challenge. Paper IV discusses current limitations in studying microbiome–metastasis crosstalk and highlights the need for advanced models. Paper V addresses this by presenting a detailed protocol for a metastatic CRC mouse model. In summary, this thesis elucidates how the gut microbiome influences CRC development and progression through multifaceted interactions within the TME. These findings underscore the potential of microbiome-targeted therapies, particularly in combating CRC.