BRD4 regulation of PIM1 identifies a novel therapeutic vulnerability in acute megakaryoblastic leukemia

Abstract Background Acute megakaryoblastic leukemia (AMKL), a rare but aggressive subtype of acute myeloid leukemia (AML), currently has limited treatment options. Given the emerging role of super-enhancers (SEs) in governing oncogenic transcriptional programs, we sought to investigate BRD4 - a key reader of SE-associated chromatin - as a potential therapeutic target in AMKL, along with identifying critical SE-regulated genes essential for AMKL survival. Methods Genetic inhibition and pharmacological degradation of BRD4 using GNE-987 were performed to assess its impact on AMKL cell proliferation and apoptosis. Through integrative multi-omics analysis, H3K27ac ChIP-seq, RNA-seq, and BRD4 CUT&TAG assays were incorporated to identify SE-associated oncogenes in AMKL. Functional validation of PIM1 genetic ablation in vitro and in vivo were performed to evaluate its role in AMKL cell viability and leukemic burden. Results BRD4 expression was significantly elevated in AMKL compared to other AML subtypes. Genetic inhibition or pharmacological degradation of BRD4 by GNE-987 potently suppressed AMKL cell proliferation and induced apoptosis, confirming BRD4 as a critical dependency in AMKL. Through integrative multi-omics analysis incorporating H3K27ac ChIP-seq, RNA-seq and BRD4 CUT&TAG, we identified PIM1 as a critical SE-associated oncogene directly regulated by BRD4 in AMKL. Importantly, PIM1 demonstrated significantly higher essentiality in AMKL compared to other AML subtypes. Functional validation revealed that PIM1 genetic ablation profoundly impaired AMKL cell viability in vitro and reduced leukemic burden in vivo. Conclusion Our work elucidates the BRD4-PIM1 axis as a critical driver of AMKL pathogenesis, wherein BRD4 maintains high PIM1 expression through SE-mediated transcriptional regulation. These findings provide a rationale for targeting BRD4 or PIM1 in precision therapy for AMKL.