E2F4/SETD1A axis-mediated METTL3 methylation promotes tumor immune evasion through impeding endogenous retroelements expression

Colorectal cancer (CRC) progression and recurrence persist as major clinical challenges despite standard therapies. Emerging evidence underscores that tumor relapse arises from crosstalk between malignant cells and the immunosuppressive microenvironment, yet the role of non-histone lysine methylation in this interplay remains unclear. Here, we identify di-methylation of lysine 513 (K513) on methyltransferase-like 3 (METTL3) as a key epigenetic modification associated with CRC progression and recurrence. Mechanistically, we reveal that SETD1A catalyzes METTL3 K513 methylation, enhancing its binding affinity to S-adenosylmethionine (SAM) and augmenting RNA m6A deposition. Strikingly, METTL3 methylation suppresses endogenous retroelements expression, leading to impaired type I interferon responses and tumor immune evasion. We further uncover a fluorouracil-induced E2F4/SETD1A/METTL3 regulatory axis, wherein E2F4 self-regulation activates SETD1A to drive METTL3 methylation. Targeting this axis through pharmacological inhibition of E2F4 or genetic disruption of METTL3 methylation synergizes with immune checkpoint blockade (ICB), significantly suppressing tumor growth. Our findings unveil a methylation-dependent regulatory mechanism that reshapes the tumor immune microenvironment, offering a novel therapeutic strategy for CRC. Overall design: To determine the biological importance of METTL3 methylation at K513, we conducted methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequence on METTL3 WT and K513R LoVo cells