BRD9 depletion-mediated ALOX5 upregulation via chromatin dysregulation induces ferroptosis in SF3B1-mutant hematopoiesis.

SF3B1 mutations are among the most common splicing factor mutations in myeloid malignancies, yet the mechanisms linking aberrant splicing to metabolic phenotypes remain incompletely understood. We previously demonstrated that SF3B1 mutations cause nonsense-mediated decay of BRD9, a core component of the non-canonical BAF chromatin remodeling complex. Here, we investigated how the SF3B1-BRD9 pathway contributes to metabolic reprogramming in hematopoietic cells. Using BRD9-depleted murine models and analyses of SF3B1-mutated samples, we found that BRD9 depletion markedly upregulates ALOX5, which plays a key role in lipid peroxidation, particularly by oxidizing polyunsaturated fatty acids. BRD9 and ALOX5 expressions are negatively correlated, and the presence of SF3B1 mutations is associated with ALOX5 upregulation in AML datasets. Notably, transcriptomic analysis demonstrated preferential upregulation of ALOX5 in mature myeloid lineages rather than stem/progenitor fractions. Mechanistically, integrated RNA-seq/ChIP-seq and Hi-C analyses revealed that BRD9 loss enhances CTCF occupancy at the ALOX5 locus boundary, enabling aberrant chromatin loop formation that drives transcriptional activation. These events increase lipid peroxidation and ferroptosis susceptibility in hematopoietic cells as evidenced by enhanced BODIPY-C11 oxidation and erastin sensitivity. Our findings reveal a spliceosome-to-chromatin-to-metabolism pathway in which SF3B1 mutations promote ferroptosis through BRD9-mediated chromatin dysregulation, highlighting the previously unrecognized metabolic rewiring in myeloid malignancies.