Aberrant activation of m6A demethylase FTO renders HIF2α clear cell renal cell carcinoma sensitive to BRD9 inhibitors.

Hypoxia-inducible factor 2α (HIF2α) antagonists are effective against clear cell renal cell carcinomas (ccRCCs) that highly express HIF2α. To identify potential drug targets in HIF2α ccRCC, we constructed an epigenetic-focused single-guide RNA library and performed an in vivo CRISPR-Cas9 knockout screen in BALB/c nude mice transplanted with 786-O (HIF2α) or Caki-2 (HIF2α) cells. We found that the m6A demethylase fat mass and obesity-associated () gene was indispensable to the growth of HIF2α but not HIF2α ccRCC. Activation of FTO in HIF2α ccRCC was caused by an increased intracellular α-ketoglutarate–to-succinate ratio and stabilized bromodomain-containing protein 9 () messenger RNA via m6A demethylation. RNA sequencing and chromatin immunoprecipitation sequencing profiling further revealed that SRY-box transcription factor 17 (SOX17) recruited BRD9 to de novo super enhancers associated with genes that feature prominently in ccRCC pathogenesis, including , , , , and . knockdown or the BRD9-selective antagonist I-BRD9 suppressed the growth of HIF2α but not HIF2α ccRCC cells in vitro. In BALB/c nude mice bearing HIF2α ccRCC cell line–derived xenografts and patient-derived tumor xenografts, I-BRD9 administration effectively inhibited tumor growth and prolonged the survival of tumor-bearing mice with greater efficacy than sunitinib. Together, these findings indicate that BRD9 is a druggable target for treating HIF2α ccRCC.