Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity
Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen
Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen
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Research Article Cell biology Genetics Oncology

Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity

Abstract

PRC2/EZH2 inhibitors (PRC2i/EZH2i) are promising for the treatment of advanced cancers including metastatic prostate cancer. Here, we show that PRC2i/EZH2i alone or in combination with androgen receptor (AR) inhibitors induced diverse cell state programs (CSPs) (e.g., response to stress or IFN, MYC targets, stem cells, EMT lineage plasticity, and multiple developmental programs), which led to increased tumor cell invasion, metastasis, and resistance to other drugs, in addition to modest suppression of tumor growth. In contrast to the current perception, our comprehensive, integrated genomics and epigenomics profiling of patient-derived xenografts (PDXs) and clinical tumors revealed that PRC2/EZH2 suppressed CSP genes by maintaining chromatin bivalency. Hyperactive Wnt/β-catenin signaling and inhibitors of polycomb-repressive complex 2/enhancer of zeste homolog 2 (PRC2/EZH2) and the AR alter chromatin bivalency through antagonism of PRC2 and stimulation of MLL2/KMT2B in a feed-forward manner. The circadian rhythm regulator REV-ERBα unexpectedly reprogrammed β-catenin in promoting bivalency resolution and CSP gene expression. Dual targeting of Wnt/β-catenin and EZH2 diminished diverse cell states by restoring bivalency and effectively blocked tumor growth. Our findings provide unexpected insights into chromatin bivalency and dysregulated circadian rhythms in the control of cell state diversity and identify alternative therapeutic strategies that target PRC2/EZH2 for advanced malignancies.

Authors

Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen

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Figure 7

Hyperactive Wnt/β-catenin and REV-ERBα promote KMT2B function and antagonize PRC2 in driving chromatin bivalency changes.

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Hyperactive Wnt/β-catenin and REV-ERBα promote KMT2B function and antago...
(A) Left: Representative images of PLA analysis of REV-ERBα, β-catenin, and KMT2B in 42DEnzR cells treated with 10 μM LGK974, 7.5 μM SR8278, or vehicle for 24 hours. Images are representative of 3 independent experiments. Right: PLA dots were quantified (mean ± SD; n = 3). Scale bar: 50 μm. ****P < 0.0001, by 2-tailed Student’s t test. (B) Venn diagram of peaks of REV-ERBα, β-catenin, and KMT2B ChIP-seq at bivalent promoters in C4-2B cells. (C) Signal profiles and heatmap of KMT2B ChIP-seq within ±3 kb windows around the TSS at bivalent promoters in C4-2B cells with ca–β-C expression, REV-ERBα OE, or vector control. (D) Signal profiles of EZH2 and EED ChIP-seq within ±3 kb windows around the TSS at bivalent promoters in 42DEnzR cells treated with vehicle,10 μM LGK974, or 7.5 μM SR8278 for 24 hours. (E) IGV snapshots of the indicated ChIP-seq at the indicated bivalent genes in C4-2B cells treated as in C and D.