GALNT7 promotes the malignant progression of gastrointestinal stromal tumors by regulating KIT O-GalNAc glycosylation

Background Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract and is mainly driven by activating KIT or PDGFRA mutations. Although tyrosine kinase inhibitors (TKIs) improve outcomes, primary and acquired resistance remain major challenges, especially in high-risk and wild-type GIST. Protein O-GalNAc glycosylation regulates protein stability and signaling, but its role in GIST remains unclear. Methods Bulk RNA-seq, proteomic, and single-cell RNA-seq data were integrated to identify O-glycosylation-related programs and key glycosyltransferases in GIST. Functional assays in GIST-T1 and GIST-882 cells, together with xenograft models, were performed to assess the effects of GALNT7. GALNT7–KIT interaction, KIT O-GalNAcylation, and protein stability were examined by co-immunoprecipitation, VVA lectin blotting, confocal microscopy, and cycloheximide chase assays. Benzyl-α-GalNAc was evaluated as an O-glycosylation-targeting strategy in vitro and in vivo. Results O-glycosylation signatures were enriched in high-risk GIST and correlated with pathological risk. High O-glycosylation scores co-segregated with elevated copy number variation in a fibroblast-like malignant cell population. GALNT7 was identified as a hub gene, was upregulated in GIST, and was associated with poor progression-free survival. GALNT7 promoted GIST cell growth, migration, and xenograft formation. Mechanistically, GALNT7 interacted with KIT, catalyzed its Tn-antigen O-GalNAcylation, increased KIT protein stability, and sustained PI3K/AKT and MAPK/ERK1/2 signaling. Benzyl-α-GalNAc reduced KIT O-GalNAcylation and stability, attenuated GALNT7-driven phenotypes, and inhibited xenograft growth. Conclusions GALNT7-mediated O-GalNAc glycosylation stabilizes KIT and drives GIST progression. GALNT7 may serve as a prognostic biomarker and therapeutic target in GIST.