A dynamic N ⁶-methyladenosine methylome regulates intrinsic and acquired resistance to tyrosine kinase inhibitors

N⁶-methyladenosine (m⁶A) on mRNAs is critical for various biological processes, yet whether m⁶A regulates drug resistance remains unknown. Here we show that developing resistant phenotypes during tyrosine kinase inhibitor (TKI) therapy depends on m⁶A reduction resulting from FTO overexpression in leukemia cells. This deregulated FTO-m⁶A axis pre-exists in naïve cell populations that are genetically homogeneous and is inducible/reversible in response to TKI treatment. Cells with mRNA m⁶A hypomethylation and FTO upregulation demonstrate more TKI tolerance and higher growth rates in mice. Either genetic or pharmacological restoration of m⁶A methylation through FTO deactivation renders resistant cells sensitive to TKIs. Mechanistically, the FTO-dependent m⁶A demethylation enhances mRNA stability of proliferation/survival transcripts bearing m⁶A and subsequently leads to increased protein synthesis. Our findings identify a novel function for the m⁶A methylation in regulating cell fate decision and demonstrate that dynamic m⁶A methylome is an additional epigenetic driver of reversible TKI-tolerance state, providing a mechanistic paradigm for drug resistance in cancer.