Abstract

Histone lactylation couples glycolytic metabolism to oncogenic transcription, but its mechanistic readers remain poorly defined. Here, we identify bromodomain-containing protein 9 (BRD9) as a lactyl-lysine reader that links lactate-driven H3K18 lactylation (H3K18la) to chromatin remodeling in hepatocellular carcinoma (HCC). Clinically, elevated H3K18la levels correlate with poor HCC prognosis. Structural (NMR) and biophysical analyses demonstrate that BRD9’s bromodomain engages H3K18la with weak, transient affinity through its conserved acetyl-lysine pocket, distinct from its stable H3K18ac binding. This enables BRD9 to function as a metabolic-epigenetic sensor, dynamically recruited to chromatin in response to glycolytic flux. Multi-omics profiling reveals that H3K18la recruits BRD9 and the non-canonical BRG1-associated factor (ncBAF) chromatin remodeling complex to active enhancers and promoters, promoting chromatin accessibility and driving oncogenic transcription ( SPARC , TMEM64 , ANGEL1 , SCARB1 ). Glycolytic inhibition or BRD9 targeting displaces BRD9 from chromatin, suppresses oncogenes, and impairs HCC proliferation. Modulating the lactylation vis p300 or HDAC inhibition attenuates transcription and reduces tumor viability. In vivo, glycolytic inhibition suppresses tumor growth. Our findings establish a feedforward loop wherein glycolytic flux promotes H3K18la-dependent BRD9-ncBAF recruitment to remodel chromatin and sustain oncogenic transcription, defining BRD9 as a critical metabolic-epigenetic mediator and a promising therapeutic target in HCC.