Patients with mesenchymal tumours and high <i>Fusobacteriales</i> prevalence have worse prognosis in colorectal cancer (CRC).

Abstract

Transcriptomic-based subtyping, consensus molecular subtyping (CMS) and colorectal cancer intrinsic subtyping (CRIS) identify a patient subpopulation with mesenchymal traits (CMS4/CRIS-B) and poorer outcome. Here, we investigated the relationship between prevalence of <i>Fusobacterium nucleatum</i> (<i>Fn</i>) and <i>Fusobacteriales</i>, CMS/CRIS subtyping, cell type composition, immune infiltrates and host contexture to refine patient stratification and to identify druggable context-specific vulnerabilities. We coupled cell culture experiments with characterisation of <i>Fn</i>/<i>Fusobacteriales</i> prevalence and host biology/microenviroment in tumours from two independent colorectal cancer patient cohorts (Taxonomy: n=140, colon and rectal cases of The Cancer Genome Atlas (TCGA-COAD-READ) cohort: n=605). In vitro, <i>Fn</i> infection induced inflammation via nuclear factor kappa-light-chain-enhancer of activated B cells/tumour necrosis factor alpha in HCT116 and HT29 cancer cell lines. In patients, high <i>Fn</i>/<i>Fusobacteriales</i> were found in CMS1, microsatellite unstable () tumours, with infiltration of M1 macrophages, reduced M2 macrophages, and high interleukin (IL)-6/IL-8/IL-1β signalling. Analysis of the Taxonomy cohort suggested that <i>Fn</i> was prognostic for CMS4/CRIS-B patients, despite having lower <i>Fn</i> load than CMS1 patients. In the TCGA-COAD-READ cohort, we likewise identified a differential association between <i>Fusobacteriales</i> relative abundance and outcome when stratifying patients in mesenchymal (either CMS4 and/or CRIS-B) versus non-mesenchymal (neither CMS4 nor CRIS-B). Patients with mesenchymal tumours and high <i>Fusobacteriales</i> had approximately twofold higher risk of worse outcome. These associations were null in non-mesenchymal patients. Modelling the three-way association between <i>Fusobacteriales</i> prevalence, molecular subtyping and host contexture with logistic models with an interaction term disentangled the pathogen-host signalling relationship and identified aberrations (including NOTCH, CSF1-3 and IL-6/IL-8) as candidate targets. This study identifies CMS4/CRIS-B patients with high <i>Fn</i>/<i>Fusobacteriales</i> prevalence as a high-risk subpopulation that may benefit from therapeutics targeting mesenchymal biology.