Integrated screens identify AURKB dependency in advanced gastrointestinal stromal tumors

The only approved systemic treatments for gastrointestinal stromal tumors (GISTs) are KIT/PDGFRA-directed tyrosine kinase inhibitors (TKIs), which eventually lead to the development of secondary polyclonal resistance mutations. Complementary treatment strategies are urgently needed. Using transcriptomic profiling, CRISPR screens, and chemical screens, we identify aurora kinase B (AURKB) as a previously less recognized therapeutic vulnerability to advanced GISTs. AURKB is frequently overexpressed in high-risk and metastatic GISTs but not in low-/intermediate-risk GISTs across our two patient cohorts, with FOXM1 responsible for AURKB overexpression. Genetic depletion of AURKB inhibits GIST proliferation and growth in vitro and in vivo. Mechanistically, our mass spectrometry–based proteomics screen further reveals that AURKB binds to and stabilizes ATAD2 via the ubiquitin–proteasome system, enhancing chromatin accessibility for DNA damage repair genes. Notably, AURKB inhibitors demonstrate potent efficacy in multiple preclinical GIST cell models and xenograft models at safe doses, overcoming TKI resistance. Our comprehensive approaches define unique AURKB-ATAD2 dependency in GISTs and identify non-receptor tyrosine kinase therapeutic strategies for clinical translation.