METTL3 loss exacerbates colitis via m⁶A-dependent Slc39a8 regulation and epithelial lineage depletion

The intestinal epithelium maintains host-microbiota homeostasis, while inflammatory conditions, such as inflammatory bowel disease (IBD), induce pathological shifts in intestinal epithelial cell (IEC) subtypes. We unveil METTL3, an RNA m⁶A methyltransferase, as a pivotal regulator of this balance. METTL3 is enriched in intestinal stem cells and transit-amplifying cells (TACs), and upregulated in patients with IBD and a mouse model of IBD. DSS-challenged, intestine-specific Mettl3 knockout mice exhibited exacerbated colitis as exemplified by more weight loss, elevated disease activity index (DAI), and higher extent of colon shortening. Single-cell transcriptomics of colonic tissues from DSS-challenged intestine-specific Mettl3 knockout mice revealed that Mettl3 ablation depleted epithelial lineages (TACs, goblet cells, enterocytes) but amplified immune infiltration (macrophages, neutrophils, T cells) within the intestinal mucosa. Crucially, METTL3 loss impaired TAC multipotency and increased epithelial-neutrophil crosstalk mediated by the TNF pathway. Mechanistically, METTL3-mediated m⁶A modification increases Slc39a8 expression, whose knockdown in colon organoids phenocopied METTL3 deficiency in impairing self-renewal. Our work establishes METTL3 as a dual guardian of intestinal homeostasis-preserving epithelial regeneration and restraining inflammation by calibrating epithelial-immune dialogue. The former is mediated at least in part by regulating Slc39a8 expression through m⁶A modification.