The E. coli CNF1 toxin induces fetal reprogramming of intestinal stem cells and a serrated colorectal cancer transcriptional signature in organoids

Mechanistic insights are essential to understand how gut microbiota pathobionts contribute to tumorigenesis, given the mounting evidence linking them to colorectal cancer. We report a higher prevalence of the Rho GTPases-targeting cnf1 toxin gene from Escherichia coli in the microbiota of early-stage, proximal colorectal cancer. Comparative gene set enrichment analysis reveals a concordant serrated pathway signature between colorectal cancer tissue of patients colonized with cnf1 ⁺ bacteria and CNF1-treated mouse intestinal organoids. RNA sequencing of organoids shows that CNF1 induces a fetal-like transcriptional reprogramming. Using integrated approaches, we demonstrate that CNF1 reprograms Lgr5⁺ stem cells into a Ly6a/Sca-1⁺ fetal-like state, that exhibits enhanced stemness potential. This reprogramming is preceded by a Yap/Taz-driven early transcriptional program and nuclear translocation of Yap. Functional analyses identify a RhoA/Rock–Yap/Taz–dependent transition to Ly6a/Sca-1⁺ stem cells, highlighting a mechanistic link between bacterial effectors and stem cell plasticity in colorectal tumorigenesis.