Targeting the SETD2-FTO-KIT pathway as a pharmacological strategy for TKI-refractory GIST

Tyrosine kinase inhibitors (TKIs) have significantly improved outcomes in gastrointestinal stromal tumors (GIST), but acquired resistance remains a major clinical obstacle. The underlying mechanisms that sustain oncogenic KIT signaling in TKI-refractory GIST are not fully understood. Here, we identify a previously unrecognized epigenetic-epitranscriptomic regulatory axis involving SETD2, FTO, and KIT that promotes TKI resistance by stabilizing KIT mRNA. FTO, a key N ⁶-methyladenosine (m⁶A) RNA demethylase, was found to be markedly overexpressed in high-risk and recurrent GIST samples and correlated with poor prognosis. Mechanistically, FTO enhances KIT mRNA stability by erasing m⁶A modification in its 3' untranslated region (UTR), thereby preventing YTHDF2-mediated degradation and sustaining oncogenic KIT expression. Furthermore, the histone methyltransferase SETD2 activates FTO transcription via H3K36 trimethylation at the FTO promoter, establishing a self-reinforcing loop that maintains FTO overexpression. Functional experiments using FTO knockout and pharmacological inhibition (CS1 and entacapone) demonstrated that disrupting FTO activity suppresses tumor proliferation, reduces KIT expression, and restores sensitivity to imatinib both in vitro and in vivo. In KIT-Asp818Tyr/+ genetically engineered GIST mouse models, the combination of entacapone and imatinib led to significant tumor regression. Most importantly, preliminary clinical results from a Phase I trial (ClinicalTrials.gov: NCT04006769) showed that treatment with entacapone plus imatinib resulted in partial remission in two out of three evaluable TKI-refractory GIST patients, supporting the translational relevance of this strategy. Collectively, our findings establish the SETD2-FTO-KIT axis as a critical mechanism driving drug resistance in GIST and reveal m⁶A demethylation as a key regulator of KIT mRNA stability. Targeting FTO represents a promising and actionable therapeutic strategy to overcome TKI resistance and improve outcomes for patients with advanced GIST.