Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage

Oncogene volume 41, pages 1397–1409 (2022)Cite this article

Subjects

Abstract

Hepatocellular carcinoma (HCC) has emerged as the third cause of cancer-related death owing to lacking effective systemic therapies. Genomic DNA sequencing revealed the high frequency of loss-of-function mutations in ARID2, which encodes a subunit of SWI/SNF chromatin remodeling complex, however, the therapeutic strategy for the HCC patients with ARID2 mutations is still completely unclear. In this study, we first performed a high-throughput screening approach using a compound library consisting of 2 180 FDA-approved drugs and other compounds, to elicit the potential drugs for synthetic lethality to target ARID2-deficient HCC cells. Interestingly, JQ1, a selective inhibitor of bromodomain protein BRD4, uniquely suppressed the growth of ARID2- deficient HCC cells. Next JQ1 is further confirmed to predominantly induce cell lethality upon ARID2 depletion through exacerbating DNA damage, especially double strand breaks (DSBs). Functional assays demonstrated that both BRD4 inhibition and ARID2 deficiency synergistically impede two main DNA damage repair pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ), through attenuating the transcription of BRCA1, RAD51, and 53BP1, which encode the core molecules responsible for DSB repair. Mechanistically, both ARID2 and BRD4 exert a synergistic effect for maintaining transcriptional enhancer-promoter loops of these genes within chromatin conformation. However, as both ARID2 and BRD4 are disrupted, the expression of these DNA repair-related genes in response to DNA damage are hindered, resulting in DSB accumulation and cell apoptosis. Taken together, this study discloses that BRD4 inhibition may induce synthetic lethality in ARID2-deficient HCC cells, which might provide a potential therapeutic strategy for HCC patients with ARID2 mutations.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: ARID2-deficient cells are hypersensitive to BET inhibitor JQ1.
Fig. 2: BRD4 inhibition confers the synthetic lethality to ARID2 deficiency in HCC cells.
Fig. 3: BRD4 inhibitor JQ1 induces the accumulation of DNA damage and cell apoptosis in ARID2-deficient HCC cells.
Fig. 4: BRD4 inhibitor JQ1 decreases HR and NHEJ activities in ARID2-deficient cells.
Fig. 5: JQ1 represses the enhancer and promoter activities of BRCA1, RAD51, and 53BP1.
Fig. 6: Both ARID2 deficiency and BRD4 inhibition synergistically impair the enhancer-promoter interactions of BRCA1, RAD51, and 53BP1.
Fig. 7: JQ1 efficiently suppresses ARID2-deficient HCC tumors in vivo.

Similar content being viewed by others

References

  1. Forner A, Reig M, Bruix J. Hepatocellular carcinoma. Lancet. 2018;391:1301–14.

    Article  PubMed  Google Scholar 

  2. Villanueva A. Hepatocellular carcinoma. N. Engl J Med. 2019;380:1450–62.

    Article  CAS  PubMed  Google Scholar 

  3. Llovet JM, Zucman-Rossi J, Pikarsky E, Sangro B, Schwartz M, Sherman M, et al. Hepatocellular carcinoma. Nat Rev Dis Prim. 2016;2:16018.

    Article  PubMed  Google Scholar 

  4. Colombo M. Hepatocellular carcinoma. J Hepatol. 1992;15:225–36.

    Article  CAS  PubMed  Google Scholar 

  5. Schulze K, Imbeaud S, Letouzé E, Alexandrov LB, Calderaro J, Rebouissou S, et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets. Nat Genet. 2015;47:505–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Schulze K, Nault J-C, Villanueva A. Genetic profiling of hepatocellular carcinoma using next-generation sequencing. J Hepatol. 2016;65:1031–42.

    Article  CAS  PubMed  Google Scholar 

  7. Masliah-Planchon J, Bièche I, Guinebretière J-M, Bourdeaut F, Delattre O. SWI/SNF chromatin remodeling and human malignancies. Annu Rev Pathol. 2015;10:145–71.

    Article  CAS  PubMed  Google Scholar 

  8. Wilson BG, Roberts CWM. SWI/SNF nucleosome remodellers and cancer. Nat Rev Cancer. 2011;11:481–92.

    Article  CAS  PubMed  Google Scholar 

  9. Mashtalir N, D’Avino AR, Michel BC, Luo J, Pan J, Otto JE, et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes. Cell. 2018;175:1272–88 e20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mittal P, Roberts CWM. The SWI/SNF complex in cancer–biology, biomarkers, and therapy. Nat Rev Clin Oncol. 2020;17:435–48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, et al. Structure of nucleosome-bound human BAF complex. Science. 2020;367:875–81.

    Article  CAS  PubMed  Google Scholar 

  12. Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, Pelletier L, Maad IB, et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet. 2012;44:694–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li M, Zhao H, Zhang X, Wood LD, Anders RA, Choti MA, et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet. 2011;43:828–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Cajuso T, Hänninen UA, Kondelin J, Gylfe AE, Tanskanen T, Katainen R, et al. Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2, and ARID4A in microsatellite unstable colorectal cancer. Int J Cancer. 2014;135:611–23.

    Article  CAS  PubMed  Google Scholar 

  15. Jiang H, Cao H-J, Ma N, Bao W-D, Wang J-J, Chen T-W, et al. Chromatin remodeling factor ARID2 suppresses hepatocellular carcinoma metastasis via DNMT1-Snail axis. Proc Natl Acad Sci USA. 2020;117:4770–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Loesch R, Chenane L, Colnot S. ARID2 chromatin remodeler in hepatocellular carcinoma. Cells. 2020;9:2152.

    Article  CAS  PubMed Central  Google Scholar 

  17. Helming KC, Wang X, Roberts CWM. Vulnerabilities of mutant SWI/SNF complexes in cancer. Cancer Cell. 2014;26:309–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Huang A, Garraway LA, Ashworth A, Weber B. Synthetic lethality as an engine for cancer drug target discovery. Nat Rev Drug Discov. 2020;19:23–38.

    Article  CAS  PubMed  Google Scholar 

  19. Chan DA, Giaccia AJ. Harnessing synthetic lethal interactions in anticancer drug discovery. Nat Rev Drug Discov. 2011;10:351–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bitler BG, Aird KM, Garipov A, Li H, Amatangelo M, Kossenkov AV, et al. Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers. Nat Med. 2015;21:231–8.

    Article  CAS  PubMed  Google Scholar 

  21. Shen J, Peng Y, Wei L, Zhang W, Yang L, Lan L, et al. ARID1A deficiency impairs the DNA damage checkpoint and sensitizes cells to PARP inhibitors. Cancer Discov. 2015;5:752–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Deribe YL, Sun Y, Terranova C, Khan F, Martinez-Ledesma J, Gay J, et al. Author correction: mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer. Nat Med. 2018;24:1627.

    Article  CAS  PubMed  Google Scholar 

  23. Caruso S, Calatayud AL, Pilet J, La Bella T, Rekik S, Imbeaud S, et al. Analysis of liver cancer cell lines identifies agents with likely efficacy against hepatocellular carcinoma and markers of response. Gastroenterology. 2019;157:760–76.

    Article  CAS  PubMed  Google Scholar 

  24. Tai Y, Gao J-H, Zhao C, Tong H, Zheng S-P, Huang Z-Y, et al. SK-Hep1: not hepatocellular carcinoma cells but a cell model for liver sinusoidal endothelial cells. Int J Clin Exp Pathol. 2018;11:2931–8.

    PubMed  PubMed Central  Google Scholar 

  25. Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER, et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019;569:503–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Arnoult N, Correia A, Ma J, Merlo A, Garcia-Gomez S, Maric M, et al. Regulation of DNA repair pathway choice in S and G2 phases by the NHEJ inhibitor CYREN. Nature. 2017;549:548–52.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Gao Q, Wang K, Chen K, Liang L, Zheng Y, Zhang Y, et al. HBx protein-mediated ATOH1 downregulation suppresses ARID2 expression and promotes hepatocellular carcinoma. Cancer Sci. 2017;108:1328–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, et al. Selective inhibition of BET bromodomains. Nature. 2010;468:1067–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung C-W, et al. Suppression of inflammation by a synthetic histone mimic. Nature. 2010;468:1119–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Slaughter MJ, Shanle EK, McFadden AW, Hollis ES, Suttle LE, Strahl BD, et al. PBRM1 bromodomains variably influence nucleosome interactions and cellular function. J Biol Chem. 2018;293:13592–603.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Li X, Baek G, Ramanand SG, Sharp A, Gao Y, Yuan W, et al. BRD4 promotes DNA repair and mediates the formation of TMPRSS2-ERG gene rearrangements in prostate cancer. Cell Rep. 2018;22:796–808.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. de Castro RO, Previato L, Goitea V, Felberg A, Guiraldelli MF, Filiberti A, et al. The chromatin-remodeling subunit Baf200 promotes homology-directed DNA repair and regulates distinct chromatin-remodeling complexes. J Biol Chem. 2017;292:8459–71.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Bonner WM, Redon CE, Dickey JS, Nakamura AJ, Sedelnikova OA, Solier S, et al. GammaH2AX and cancer. Nat Rev Cancer. 2008;8:957–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ceccaldi R, Rondinelli B, D’Andrea AD. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 2016;26:52–64.

    Article  CAS  PubMed  Google Scholar 

  35. Yang L, Zhang Y, Shan W, Hu Z, Yuan J, Pi J et al. Repression of BET activity sensitizes homologous recombination-proficient cancers to PARP inhibition. Sci Transl Med. 2017; 9.

  36. Donati B, Lorenzini E, Ciarrocchi A. BRD4 and cancer: going beyond transcriptional regulation. Mol Cancer. 2018;17:164.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Devaiah BN, Case-Borden C, Gegonne A, Hsu CH, Chen Q, Meerzaman D, et al. BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol. 2016;23:540–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kakarougkas A, Ismail A, Chambers AL, Riballo E, Herbert AD, Kunzel J, et al. Requirement for PBAF in transcriptional repression and repair at DNA breaks in actively transcribed regions of chromatin. Mol Cell. 2014;55:723–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Michel BC, D’Avino AR, Cassel SH, Mashtalir N, McKenzie ZM, McBride MJ, et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat Cell Biol. 2018;20:1410–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, et al. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet. 2011;7:e1002008.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Kaelin WG. The concept of synthetic lethality in the context of anticancer therapy. Nat Rev Cancer. 2005;5:689–98.

    Article  CAS  PubMed  Google Scholar 

  42. Hartwell LH, Szankasi P, Roberts CJ, Murray AW, Friend SH. Integrating genetic approaches into the discovery of anticancer drugs. Science. 1997;278:1064–8.

    Article  CAS  PubMed  Google Scholar 

  43. Friend SH, Oliff A. Emerging uses for genomic information in drug discovery. N. Engl J Med. 1998;338:125–6.

    Article  CAS  PubMed  Google Scholar 

  44. Fece de la Cruz F, Gapp BV, Nijman SMB. Synthetic lethal vulnerabilities of cancer. Annu Rev Pharm Toxicol. 2015;55:513–31.

    Article  CAS  Google Scholar 

  45. Li S, Topatana W, Juengpanich S, Cao J, Hu J, Zhang B, et al. Development of synthetic lethality in cancer: molecular and cellular classification. Signal Transduct Target Ther. 2020;5:241.

    Article  PubMed  PubMed Central  Google Scholar 

  46. Farmer H, McCabe N, Lord CJ, Tutt ANJ, Johnson DA, Richardson TB, et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature. 2005;434:917–21.

    Article  CAS  PubMed  Google Scholar 

  47. Bryant HE, Schultz N, Thomas HD, Parker KM, Flower D, Lopez E, et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature. 2005;434:913–7.

    Article  CAS  PubMed  Google Scholar 

  48. Eustermann S, Wu WF, Langelier MF, Yang JC, Easton LE, Riccio AA, et al. Structural basis of detection and signaling of DNA single-strand breaks by human PARP-1. Mol Cell. 2015;60:742–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Oba A, Shimada S, Akiyama Y, Nishikawaji T, Mogushi K, Ito H, et al. ARID2 modulates DNA damage response in human hepatocellular carcinoma cells. J Hepatol. 2017;66:942–51.

    Article  CAS  PubMed  Google Scholar 

  50. Kadoch C, Hargreaves DC, Hodges C, Elias L, Ho L, Ranish J, et al. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat Genet. 2013;45:592–601.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Berns K, Caumanns JJ, Hijmans EM, Gennissen AMC, Severson TM, Evers B, et al. ARID1A mutation sensitizes most ovarian clear cell carcinomas to BET inhibitors. Oncogene. 2018;37:4611–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Bitler BG, Wu S, Park PH, Hai Y, Aird KM, Wang Y, et al. ARID1A-mutated ovarian cancers depend on HDAC6 activity. Nat Cell Biol. 2017;19:962–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Williamson CT, Miller R, Pemberton HN, Jones SE, Campbell J, Konde A, et al. ATR inhibitors as a synthetic lethal therapy for tumours deficient in ARID1A. Nat Commun. 2016;7:13837.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, et al. ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity, and breast cancer treatment response. Nat Genet. 2020;52:187–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Fujisawa T, Filippakopoulos P. Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol. 2017;18:246–62.

    Article  CAS  PubMed  Google Scholar 

  56. Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S et al. BET Bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol Cell 2017; 67.

  57. Bhagwat AS, Roe J-S, Mok BYL, Hohmann AF, Shi J, Vakoc CR. BET bromodomain inhibition releases the mediator complex from select cis-regulatory elements. Cell Rep. 2016;15:519–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Doroshow DB, Eder JP, LoRusso PM. BET inhibitors: a novel epigenetic approach. Ann Oncol. 2017;28:1776–87.

    Article  CAS  PubMed  Google Scholar 

  59. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell. 2011;146:904–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Puissant A, Frumm SM, Alexe G, Bassil CF, Qi J, Chanthery YH, et al. Targeting MYCN in neuroblastoma by BET bromodomain inhibition. Cancer Discov. 2013;3:308–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Shu S, Wu H-J, Ge JY, Zeid R, Harris IS, Jovanović B et al. Synthetic lethal and resistance interactions with BET bromodomain inhibitors in triple-negative breast cancer. Mol Cell. 2020; 78.

  62. Stratikopoulos EE, Dendy M, Szabolcs M, Khaykin AJ, Lefebvre C, Zhou M-M, et al. Kinase and BET inhibitors together clamp inhibition of PI3K signaling and overcome resistance to therapy. Cancer Cell. 2015;27:837–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kurimchak AM, Shelton C, Duncan KE, Johnson KJ, Brown J, O’Brien S, et al. Resistance to BET bromodomain inhibitors is mediated by kinome reprogramming in ovarian cancer. Cell Rep. 2016;16:1273–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Stuhlmiller TJ, Miller SM, Zawistowski JS, Nakamura K, Beltran AS, Duncan JS, et al. Inhibition of lapatinib-induced kinome reprogramming in ERBB2-positive breast cancer by targeting BET family bromodomains. Cell Rep. 2015;11:390–404.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Centore RC, Sandoval GJ, Soares LMM, Kadoch C, Chan HM. Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies. Trends Genet. 2020;36:936–50.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank all members of Han Lab for helpful discussions on the project. This work was supported by Grants from the National Natural Science Foundation of China (82073116 and 81672772 to ZH), National Key Research and Development Program of China (2020YFC2002705 to ZH), Natural Science Foundation of Shanghai (19140902500 to ZH), National Science and Technology Major Project (2017ZX10203207 to ZH) and Shanghai Jiao Tong University Scientific and Technological Innovation Funds (2019TPA09 and ZH2018ZDA33 to ZH).

Author information

Author notes

  1. These authors contributed equally: Dan-Dan He, Xue-Ying Shang, Na Wang.

Authors and Affiliations

  1. Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China

    Dan-Dan He, Xue-Ying Shang, Na Wang, Guang-Xing Wang, Kun-Yan He, Lan Wang & Ze-Guang Han

  2. Hangzhou Innovation Institute for Systems Oncology (HIISCO), 3F Building 1, 2636 Yuhangtang Rd, Yuhang District, Hangzhou, 311121, Zhejiang Province, China

    Ze-Guang Han

Authors
  1. Dan-Dan He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xue-Ying Shang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Na Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guang-Xing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kun-Yan He
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ze-Guang Han
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

ZGH, DDH, and XYS conceived and designed this study; DDH, XYS, NW, GXW, KYH, and LW performed experiments and acquired data; DDH, XYS analyzed data and wrote manuscript; ZGH substantively revised the manuscript; ZGH supervised the project. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ze-Guang Han.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

He, DD., Shang, XY., Wang, N. et al. BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage. Oncogene 41, 1397–1409 (2022). https://doi.org/10.1038/s41388-022-02176-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41388-022-02176-2

This article is cited by

Search

Advanced search

Quick links