Opposing functions of BRD4 isoforms in breast cancer

Bromodomain-containing protein 4 (BRD4) is a cancer therapeutic target in many ongoing clinical trials disrupting primarily BRD4-regulated transcription programs. A critical role of BRD4 in cancer development has been reported and attributed mainly to the abundant long isoform (BRD4-L). Here we show, by isoform-specific knockdown and endogenous protein detection along with transgene expression, the less abundant BRD4 short isoform (BRD4-S) is oncogenic while BRD4-L is tumor-suppressive in breast cancer cell proliferation and migration as well as mammary tumor formation and metastasis. Through integrated RNA-seq transcriptome and genome-wide ChIP-seq and CUT&RUN association profiling, we identify Engrailed-1 (EN1) homeobox transcription factor as a key BRD4-S coregulator particularly in triple-negative breast cancer. BRD4-S and EN1 co-modulate the extracellular matrix (ECM)-associated matrisome network, including type II cystatin gene cluster, mucin 5 and cathepsin loci, via enhancer regulation of cancer-associated genes and pathways. Our work highlights the importance of targeted therapy for the oncogenic but not tumor-suppressive activity of BRD4. Overall design: Whole-genome expression profiling by RNA-seq with BRD4 pan or isoform-specific siRNA knockdown in MCF-7 and MDA-MB-231 cells and genome-wide binding profilling of BRD4 isoforms and EN1 by ChiP-seq and CUT&RUN in MDA-MB-231 and also in its derived line (named 3f:S) ecopotically expressing three FLAG-tagged BRD4-S with or without JQ1 treatment