METTL3 Methylation Induces Decay of Endogenous Retroelement Transcripts to Promote Tumor Immune Evasion

Colorectal cancer (CRC) progression and recurrence persist as major clinical challenges. Emerging evidence underscores that crosstalk between malignant cells and the immunosuppressive microenvironment facilitates tumor relapse, and elucidating the mechanistic details of this crosstalk could help guide development of improved therapies. Here, we identified di-methylation of lysine 513 (K513) on methyltransferase-like 3 (METTL3) as a key modification associated with CRC progression and recurrence. Mechanistically, SETD1A catalyzed METTL3 K513 methylation, enhancing its binding affinity to S-adenosylmethionine (SAM) and augmenting RNA m⁶A deposition. METTL3 methylation suppressed endogenous retroelements expression, leading to impaired type I interferon responses and tumor immune evasion. Fluorouracil induced an E2F4/SETD1A/METTL3 regulatory axis, wherein E2F4 self-regulation activated SETD1A to drive METTL3 methylation. Targeting this axis through pharmacological inhibition of E2F4 or genetic disruption of METTL3 methylation cooperated with immune checkpoint blockade (ICB) to significantly suppress tumor growth. These findings unveil a methylation-dependent regulatory mechanism that reshapes the tumor immune microenvironment, offering a therapeutic strategy for CRC.