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CDK7 blockade suppresses super‐enhancer‐associated oncogenes in bladder cancer

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Abstract

Purpose

Transcriptional addiction plays a pivotal role in maintaining the hallmarks of cancer cells. Thus, targeting super-enhancers (SEs), which modulate the transcriptional activity of oncogenes, has become an attractive strategy for cancer therapy. As yet, however, the molecular mechanisms of this process in bladder cancer (BC) remain to be elucidated. Here, we aimed to provide detailed information regarding the SE landscape in BC and to investigate new potential pharmaceutical targets for BC therapy.

Methods

We employed THZ1 as a potent and specific CDK7 inhibitor. In vitro and in vivo studies were carried out to investigate the anticancer and apoptosis-inducing effects of THZ1 on BC cells. Whole-transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) were performed to investigate the mechanism and function of SE-linked oncogenic transcription in BC cells.

Results

We found that THZ1 serves as an effective and potent inhibitor with suppressive activity against BC cells. An integrative analysis of THZ1-sensitive and SE-associated oncogenes yielded potential new pharmaceutical targets, including DDIT4, B4GALT5, PSRC1 and MED22. Combination treatment with THZ1 and the DDIT4 inhibitor rapamycin effectively suppressed BC cell growth. In addition, we found that THZ1 and rapamycin sensitized BC cells to conventional chemotherapy.

Conclusions

Our data indicate that exploring BC gene regulatory mechanisms associated with SEs through integrating RNA-seq and ChIP-seq data improves our understanding of BC biology and provides a basis for innovative therapies.

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Acknowledgements

The present study was funded by the National Key R&D Program of China (2018YFA0902800), the National Natural Science Foundation of China (81772754), the Major Basic Research and Cultivation Program of Natural Science Foundation of Guangdong Province (2017A03038009), the Shenzhen Basic Science Research program (JCYJ20190809164617205), the Sanming Project of Medicine in Shenzhen (SZSM202011011), Shenzhen Key Laboratory Program (ZDSYS20190902092857146), the Hospital Research Fund of SAHSYSU (ZSQYLCKYJJ202019) and a Research Start-up Fund of part-time PI, SAHSYSU (ZSQYJZPI202003).

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Author notes

  1. Yafei Yang, Donggen Jiang and Ziyu Zhou contributed equally to this work.

Authors and Affiliations

  1. Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China

    Yafei Yang, Donggen Jiang, Haiyun Xiong, Xiangwei Yang, Hanqi Lei & Jun Pang

  2. Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China

    Ziyu Zhou, Guoyu Peng, Wuchao Xia, Shang Wang & Song Wu

  3. Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China

    Ziyu Zhou, Guoyu Peng, Wuchao Xia, Shang Wang & Song Wu

  4. Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518107, China

    Jing Zhao & Zhirong Qian

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  1. Yafei Yang
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  2. Donggen Jiang
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  12. Song Wu
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  13. Jun Pang
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Contributions

Song Wu and Jun Pang designed the experiments. Yafei Yang, Donggen Jiang and Ziyu Zhou collected the data and analyzed the results. Haiyun Xiong, Xiangwei Yang, Guoyu Peng, Wuchao Xia, Shang Wang, Hanqi Lei, Jing Zhao and Zhirong Qian provided conceptual advice. Yafei Yang, Donggen Jiang and Ziyu Zhou wrote the paper. Song Wu and Jun Pang reviewed and edited the manuscript. Song Wu and Jun Pang obtained funding. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Song Wu or Jun Pang.

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The authors declare that they have no conflicts of interest.

Research involving human participants and/or animals

This study was approved by the ethics committee of the Seventh Affiliated Hospital of Sun Yat-sen University. All animal experiments were performed in accordance with the established guidelines of the Animal Research Ethics Committee of the Seventh Affiliated Hospital of Sun Yat-sen University.

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Supplementary Information

Supplementary Fig. 1

(a) Docking model of THZ1 in the ATP-binding pocket of CDK7. CDK7 marked with green and THZ1 depicted with iridescence, the binding site Cys312 is in red. (b) MGH-U3, 5637 and human urothelial SV-HUC-1 cells were treated with 100 nM THZ1, cell morphology and (c) colony forming ability were recorded. (d) Apoptosis analysis in MGH-U3 and 5637 cell lines treated with escalating doses for 48 h. (e) mRNA expression of representative transcripts (DDIT4, B4GALT5, EGFR and MED22) across various types of human cancer cells. Data were retrieved from the TCGA and GTEX projects (PNG 3783 kb)

High Resolution Image (TIF 12551 kb)

Supplementary Fig. 2

The correlation between selected candidate oncogene transcript levels and the OS of BC patients from public data sets plotted by the Kaplan-Meier method (PNG 514 kb)

High Resolution Image (TIF 2909 kb)

Supplementary Fig. 3

Sequence verification of CRISPR targeting regions in the indicated genes (PNG 1457 kb)

High Resolution Image (TIF 4999 kb)

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Yang, Y., Jiang, D., Zhou, Z. et al. CDK7 blockade suppresses super‐enhancer‐associated oncogenes in bladder cancer. Cell Oncol. 44, 871–887 (2021). https://doi.org/10.1007/s13402-021-00608-x

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