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

N-6-methyladenosine (m(6)A) on mRNAs is critical for various biological processes, yet whether m(6)A regulates drug resistance remains unknown. Here we show that developing resistant phenotypes during tyrosine kinase inhibitor (TKI) therapy depends on m(6)A reduction resulting from FTO overexpression in leukemia cells. This deregulated FTO-m(6)A axis pre-exists in naive cell populations that are genetically homogeneous and is inducible/reversible in response to TKI treatment. Cells with mRNA m(6)A hypomethylation and FTO upregulation demonstrate more TKI tolerance and higher growth rates in mice. Either genetic or pharmacological restoration of m(6)A methylation through FTO deactivation renders resistant cells sensitive to TKIs. Mechanistically, the FTO-dependent m(6)A demethylation enhances mRNA stability of proliferation/survival transcripts bearing m(6)A and subsequently leads to increased protein synthesis. Our findings identify a novel function for the m(6)A methylation in regulating cell fate decision and demonstrate that dynamic m(6)A methylome is an additional epigenetic driver of reversible TKI-tolerance state, providing a mechanistic paradigm for drug resistance in cancer.