15 / 2024-08-29 23:01:51

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

super-silencer,chromatin interactions,cancer

Ying Zhang^1,2*, Kaijing Chen³*, Seng Chuan Tang^1,3*, Yichao Cai¹*, Akiko Nambu¹, Yi Xiang See^1,3, Chaoyu Fu⁴, Anandhkumar Raju⁵, Benjamin Lebeau³, Zixun Ling¹, Jia Jia Chan¹, Yvonne Tay^1,6, Marek Mutwil³, Manikandan Lakshmanan⁵, Greg Tucker-Kellogg^7,8, Chng Wee Joo^1,9,10,11, Daniel G. Tenen^1,12, Motomi Osato¹, Vinay Tergaonkar^5,12, Melissa Jane Fullwood<sup>1,3,13

1</sup>Cancer Science Institute of Singapore, National University of Singapore, 14 Medical

Drive, 117599 Singapore.

²Genome Institute of Singapore, Agency for Science, Technology and Research

(A*STAR), 138672 Singapore.

³School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,

637551 Singapore.

⁴Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1,

117411 Singapore.

⁵Laboratory of NFkB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency

for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673

Singapore.

⁶Department of Biochemistry, Yong Loo Lin School of Medicine, National University of

Singapore (NUS), 8 Medical Drive, MD7, 117596 Singapore.

⁷Department of Biological Sciences, National University of Singapore, 16 Science

Drive 4, 117558 Singapore.

⁸Computational Biology Programme, Faculty of Science, National University of

Singapore, 16 Science Drive 4, 117558 Singapore.

⁹Department of Medicine, Yong Loo Lin School of Medicine, National University of

Singapore, 117597 Singapore.

¹⁰NUS Centre for Cancer Research (N2CR), Centre for Translational Medicine, 14

Medical Drive, 117599 Singapore.

¹¹Department of Hematology-Oncology, National University Cancer Institute of

Singapore (NCIS), National University Health System (NUHS), 1E Kent Ridge Road,

119228 Singapore.

¹²Harvard Stem Cells Institute, Harvard Medical School, Boston, MA 02115, USA.

¹³Institute of Molecular and Cell Biology, Agency for Science, Technology and

Research (A*STAR), 61 Biopolis Drive, Proteos, 138673 Singapore.

* These authors contributed equally



Human silencers have been identified as regulators of developmental gene expression, but their functional importance, including their potential to form “super-silencers” and their link to cancer progression, remains unclear. In this study, we demonstrate that two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a “super-silencer.” These “super-silencers” play a crucial role in controlling cancer progression, providing a compelling rationale for targeting them in cancer therapy. To disrupt these “super-silencers,” we employed a combination treatment of an EZH2 inhibitor, GSK343, and a REST inhibitor, X5050, referred to as “GR.” Remarkably, GR treatment caused a substantial loss of topologically associating domains (TADs) and chromatin loops, while synergistically upregulating super-silencer-controlled genes associated with the cell cycle, apoptosis, and DNA damage. These changes resulted in significant anticancer effects in vivo. Using time-course Hi-C and RNA-Seq analyses, we observed that the reduction in CTCF and TOP2A levels might explain the 3D genome reorganization induced by GR treatment. Overall, our findings provide evidence of a “super-silencer” and demonstrate that GR can effectively disrupt these elements, potentially leading to cancer ablation. This work has recently been accepted by Nature Structural & Molecular Biology.