Introduction
Both gut microbiome dysbiosis and dysregulated RNA N6-methyladenosine (m6A) modification have been independently linked to colorectal cancer (CRC) pathogenesis. Yet, how these two key factors interact during early CRC development remains unclear.
Aims & Methods
Aims: This study investigates YTHDF1 as a novel link between m6A epitranscriptomics and gut microbiome dysbiosis in CRC development.
Methods: We performed comparative transcriptomic analysis of YTHDF1 expression in normal colon tissue (n = 65), adenoma (n = 69), and carcinoma (n = 74) specimens from human cohorts. Intestine-specific Ythdf1 knock-in (Ythdf1cki) mice were generated to assess the effects of YTHDF1 on gut microbiota and metabolites by shotgun metagenomic sequencing and LC-MS/MS metabolomics, respectively. Fecal microbiota transplantation (FMT) from Ythdf1cki mice into germ-free and antibiotic-treated SPF mice was conducted to evaluate microbiota-driven tumorigenesis. Two independent human CRC cohorts, a publicly available dataset (PRJNA941834, n = 110) and a local Hong Kong cohort (n = 208), were analyzed to correlate YTHDF1 expression with microbial shifts, particularly taxa A, a CRC-associated bacterium. MTT assays assessed the effects of taxa A and its metabolites on CRC cell proliferation in vitro. The ApcMin/+model was used to test the tumor-promoting role of taxa A in vivo.
Results
Among m6A regulators, YTHDF1 exhibited progressive upregulation from adenoma to CRC, suggesting an early role in tumorigenesis. Compared to WT littermates, Ythdf1cki mice displayed gut dysbiosis and metabolic alteration prior to tumor development, characterized by enrichment of 18 bacterial species and 21 metabolites alongside depletion of 8 bacterial species and 49 metabolites. FMT from Ythdf1cki mice accelerated tumorigenesis in both ApcMin/+ mice and the AOM/DSS model, including antibiotic-treated SPF or germ-free recipients. Notably, Ythdf1cki recipients showed elevated serum levels of FITC-Dextran, LPS, and LBP, coupled with reduced expression of E-cadherin, indicating compromised gut barrier integrity. Furthermore, Ythdf1cki FMT enhanced colonic epithelial proliferation (indicated by elevated Ki67+ cells per crypt) and amplified pro-inflammatory responses, including marked activation of NF-κB, IL-17, and TNF-α signalings. Similarly, fecal metabolites derived from Ythdf1cki mice significantly enhanced CRC cell proliferation compared to WT metabolites. Together, these findings establish that intestinal YTHDF1 upregulation promotes CRC initiation by remodeling the gut microbiota and metabolome. Notably, taxa A, a CRC-enriched bacterium, showed significant expansion in both Ythdf1cki mice and recipient mice following FMT from Ythdf1cki donors. Consistently, we observed a significant positive correlation between both YTHDF1 mRNA (PRJNA941834 dataset, p < 0.01, Spearman' s ρ = 0.34) and protein expression (Hong Kong cohort, p < 0.05, Spearman' s ρ = 0.1705) with taxa A abundance in human CRC specimens, suggesting evolutionary conservation of YTHDF1's regulation over this bacterium from mice to humans. Further functional validation demonstrated that taxa A and its metabolites promoted CRC cell proliferation in vitro. These findings were corroborated in vivo, where taxa A significantly increased intestinal tumor burden in ApcMin/+mice.
Conclusion
Our study identifies YTHDF1 as a novel regulator of the gut microbiota, specifically enriching taxa A, which drives CRC initiation. These findings reveal a m6A-microbiota axis in early colorectal tumorigenesis, offering potential therapeutic targets.