Biofilms and core pathogens shape the tumour microenvironment and immune phenotype in colorectal cancer

Abstract

ABSTRACTObjectiveGrowing evidence links bacterial dysbiosis with colorectal cancer (CRC) carcinogenesis, characterized by an increased presence of core pathogens such asBacteroides fragilisandFusobacterium nucleatum. Here, we characterized thein situbiogeography and transcriptional interactions between bacteria and the host in mucosal colon biopsies.DesignThe influence of CRC core pathogens and biofilms on the tumour microenvironment (TME) was investigated in biopsies from patients with and without CRC (paired normal tissue and healthy tissue biopsies) using fluorescencein situhybridization and dual-RNA sequencing.ResultsTissue-invasive, mixed-species biofilms enriched forB. fragilisandF. nucleatumwere observed in CRC tissue, especially in right-sided tumours.Fusobacterium spp.was associated with increased bacterial biomass and inflammatory response in CRC samples. CRC samples with high bacterial activity demonstrated increased expression of pro-inflammatory cytokines, defensins, matrix-metalloproteases, and immunomodulatory factors. In contrast, the gene expression profiles of CRC samples with low bacterial activity resembled healthy tissue samples. Moreover, immune cell profiling showed thatB. fragilisandF. nucleatummodulated the TME and correlated with increased infiltration of neutrophils and CD4+T-cells. Overall, bacterial activity was critical for the immune phenotype and correlated with the infiltration of several immune cell subtypes, including M2 macrophages and regulatory T-cells.ConclusionBiofilms and core pathogens shape the TME and immune phenotype in CRC. Our results support thatFusobacterium spp. may provide a future therapeutic target to reduce biofilms and the inflammatory response in the TME while highlighting the importance of widening the scope of bacterial pathogenesis in CRC beyond core pathogens.