Bacteroides fragilis Toxin Suppresses METTL3-Mediated m6A Modification in Macrophage to Promote Inflammatory Bowel Disease

Abstract Background and aims Bacteroides fragilis toxin (BFT), produced by enterotoxigenic B. fragilis (ETBF), is crucial for ETBF-induced colitis. This study aims to investigate the impact of BFT–host interactions on N6-methyladenosine (m6A) modification of host mRNA and its underlying mechanisms. Methods Single-cell sequencing was employed to identify the cell types involved in ETBF-induced colitis in inflammatory bowel disease patients and dextran sodium sulfate-induced colitis mice. An ETBF strain with the bft gene deleted (ETBF[Δbft]) was utilized to investigate the role of ETBF components. The biological functions and mechanisms of BFT-induced m6A modifications, as well as the target genes, were explored in vitro and in vivo. Results Inflammatory macrophages are enriched in the intestinal mucosal tissue of both inflammatory bowel disease patients and mice with high levels of ETBF. Additionally, ETBF triggers the activation of inflammatory macrophages, subsequently inducing downstream inflammatory responses. Remarkably, BFT secreted by ETBF reduced METTL3 transcription by inhibiting FOXD3 expression and induced a dramatic reduction of m6A modifications in inflammatory macrophages. Moreover, BFT promotes the expression of its target ITGA5 expression by diminishing YTHDF2-dependent mRNA degradation. Targeting integrin subunit alpha 5 using Cilengitide significantly alleviated ETBF-induced colitis by decreasing the level of inflammatory factors in macrophages. Conclusions Our study reveals that BFT produced by ETBF leads to a reduction of m6A modifications by reducing METTL3 transcription and promotes ITGA5 expression in inflammatory macrophages. These findings provide new insights into the modulation of human m6A epitranscriptome in macrophages by gut microbiota and its significance in inflammatory bowel disease progression.