@article{dd44f28a52644260b7dfa8be2babb7d5,
title = "Opposing Functions of BRD4 Isoforms in Breast Cancer",
abstract = "Bromodomain-containing protein 4 (BRD4) is a cancer therapeutic target in ongoing clinical trials disrupting primarily BRD4-regulated transcription programs. The role of BRD4 in cancer has been 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, genome-wide ChIP-seq, and CUT&RUN association profiling, we identify the Engrailed-1 (EN1) homeobox transcription factor as a key BRD4-S coregulator, particularly in triple-negative breast cancer. BRD4-S and EN1 comodulate 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 therapies for the oncogenic, but not tumor-suppressive, activity of BRD4.",
keywords = "BET inhibitor, BRD4, CUT&RUN, ECM, TNBC, bromodomain, drug resistance, enhancer, epigenetics, transcription factor",
author = "Wu, {Shwu Yuan} and Lee, {Chien Fei} and Lai, {Hsien Tsung} and Yu, {Cheng Tai} and Lee, {Ji Eun} and Hao Zuo and Tsai, {Sophia Y.} and Tsai, {Ming Jer} and Kai Ge and Yihong Wan and Chiang, {Cheng Ming}",
note = "Funding Information: We thank Steven Henikoff for providing pA-MNase protein and spike-in yeast DNA used in CUT&RUN; Khandan Keyomarsi, Ganesh Raj, Srinivas Malladi, and Weibo Luo for select BCa cell lines; Scott Floyd for BRD4 isoform B (i.e. short form b) cDNA; Jessica Castaneda-Gill for assistance in animal work; Venkat Malladi, Anusha Nagari, and Beibei Chen for bioinformatics help; Ling Cai for guidance in patient survival and TCGA analysis; and Hongtao Yu, Jian Xu, Min Ni, and Xie Wei for discussion. We also thank NGS Core for sequencing and help in RNA-seq analysis, as well as BioHPC for accessing genome-wide analysis platforms. We are grateful for William Chiang, Louise Chow, Thomas Wilkie, Hongtao Yu, and Jian Xu for comments on the manuscript and particularly Jian Xu and Miao Cui for discussion about CUT&RUN. This work was supported in part by NIH grant 1RO1CA251698-01, CPRIT grants RP180349 and RP190077, and Welch Foundation grant I-1805 (to C.-M.C.). The research in Y.W.{\textquoteright}s lab is supported by grants from NIH (RO1CA229487 and R01CA236802), DOD (W81XWH-18-1-0014), CPRIT (RP180047), and Welch Foundation (I-1751). Y.W. is Lawrence Raisz Professor in Bone Cell Metabolism and a Virginia Murchison Linthicum Scholar in Medical Research. S.-Y.W. designed and carried out most cell-based, RNA-seq, and CUT&RUN experiments; performed interaction assays; analyzed RNA-seq, ChIP-seq, CUT&RUN data and patient expression profiles; prepared figures; and wrote the initial manuscript. C.-F.L. performed BRD4 transgenic and xenograft mouse experiments; generated lentivirus and stable cell lines expressing shRNA, sgRNA, dCas9-KRAB, 3f:BRD4-S, or 3f:BRD4-L; and conducted initial cell-cycle fluorescence-activated cell sorting (FACS) analysis. H.-T.L. conducted cell migration assay, independent cell-cycle FACS analysis, BLI mouse imaging, and animal dissection. C.-T.Y. generated BRD4-S and BRD4-L ESCs and BRD4-S transgenic mice. J.-E.L. performed ChIP-seq and provided pMSCVhyg_3xT7_PA1 and guidance on ChIP-seq data analysis. H.Z. performed LM2 and 1833 injection and initial LM2 xenograft mouse experiments. S.Y.T. M.-J.T. and Y.W. provided guidance in mouse experiments. K.G. provided guidance for ChIP-seq data interpretation. C.-M.C. supervised all aspects of the research and wrote the final manuscript. All authors were involved in data discussion and commenting on the manuscript. The authors declare no competing interests. Funding Information: We thank Steven Henikoff for providing pA-MNase protein and spike-in yeast DNA used in CUT&RUN; Khandan Keyomarsi, Ganesh Raj, Srinivas Malladi, and Weibo Luo for select BCa cell lines; Scott Floyd for BRD4 isoform B (i.e., short form b) cDNA; Jessica Castaneda-Gill for assistance in animal work; Venkat Malladi, Anusha Nagari, and Beibei Chen for bioinformatics help; Ling Cai for guidance in patient survival and TCGA analysis; and Hongtao Yu, Jian Xu, Min Ni, and Xie Wei for discussion. We also thank NGS Core for sequencing and help in RNA-seq analysis, as well as BioHPC for accessing genome-wide analysis platforms. We are grateful for William Chiang, Louise Chow, Thomas Wilkie, Hongtao Yu, and Jian Xu for comments on the manuscript and particularly Jian Xu and Miao Cui for discussion about CUT&RUN. This work was supported in part by NIH grant 1RO1CA251698-01 , CPRIT grants RP180349 and RP190077 , and Welch Foundation grant I-1805 (to C.-M.C.). The research in Y.W.{\textquoteright}s lab is supported by grants from NIH ( RO1CA229487 and R01CA236802 ), DOD ( W81XWH-18-1-0014 ), CPRIT ( RP180047 ), and Welch Foundation ( I-1751 ). Y.W. is Lawrence Raisz Professor in Bone Cell Metabolism and a Virginia Murchison Linthicum Scholar in Medical Research. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",
year = "2020",
month = jun,
day = "18",
doi = "10.1016/j.molcel.2020.04.034",
language = "English (US)",
volume = "78",
pages = "1114--1132.e10",
journal = "Molecular cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "6",
}