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The BAP1 nuclear deubiquitinase is involved in the nonhomologous end-joining pathway of double-strand DNA repair through interaction with DNA-PK

Oncogene volume 43, pages 1087–1097 (2024)Cite this article

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Abstract

BRCA1-associated protein 1 (BAP1) has emerged as a major tumor suppressor gene in diverse cancer types, notably in malignant pleural mesothelioma (DPM), and has also been identified as a germline cancer predisposition gene for DPM and other select cancers. However, its role in the response to DNA damage has remained unclear. Here, we show that BAP1 inactivation is associated with increased DNA damage both in Met-5A human mesothelial cells and human DPM cell lines. Through proteomic analyses, we identified PRKDC as an interaction partner of BAP1 protein complexes in DPM cells and 293 T human embryonic kidney cells. PRKDC encodes the catalytic subunit of DNA protein kinase (DNA-PKcs) which functions in the nonhomologous end-joining (NHEJ) pathway of DNA repair. Double-stranded DNA damage resulted in prominent nuclear expression of BAP1 in DPM cells and phosphorylation of BAP1 at serine 395. A plasmid-based NHEJ assay confirmed a significant effect of BAP1 knockdown on cellular NHEJ activity. Combination treatment with X-ray irradiation and gemcitabine (as a radiosensitizer) strongly suppressed the growth of BAP1-deficient cells. Our results suggest reciprocal positive interactions between BAP1 and DNA-PKcs, based on phosphorylation of BAP1 by the latter and deubiquitination of DNA-PKcs by BAP1. Thus, functional interaction of BAP1 with DNA-PKcs supports a role for BAP1 in NHEJ DNA repair and may provide the basis for new therapeutic strategies and new insights into its role as a tumor suppressor.

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Fig. 1: Comet assay analysis for genomic instability caused by genomic alteration of BAP1.
Fig. 2: Analysis of BAP1 interacting proteins by Interactional Total Peptide (ITOP) analysis.
Fig. 3: Analysis of phosphorylation sites on BAP1.
Fig. 4: BAP1 protein expression in the (a–h) mesothelium cell MeT-5A and (i–p) DPM cell line H-Meso.
Fig. 5: Relationship between BAP1 and DNA-PK.
Fig. 6: Therapeutic potential of targeting latent genomic instability induced by BAP1 loss in DPM.

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References

  1. Febres-Aldana CA, Fanaroff R, Offin M, Zauderer MG, Sauter JL, Yang SR, et al. Diffuse pleural mesothelioma: advances in molecular pathogenesis, diagnosis and treatment. Ann Rev Pathol. 2023. https://doi.org/10.1146/annurev-pathol-042420-092719.

    Article  Google Scholar 

  2. Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, et al. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet. 2011;43:668–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, et al. Integrative molecular characterization of malignant pleural mesothelioma. Cancer Discov. 2018;812:1548–65.

    Article  Google Scholar 

  4. Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, Worley LA, et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science. 2010;330:1410–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jensen DE, Proctor M, Marquis ST, Gardner HP, Ha SI, Chodosh LA, et al. BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene. 1998;16:1097–112.

    Article  CAS  PubMed  Google Scholar 

  6. Testa JR, Cheung M, Pei J, Below JE, Tan Y, Sementino E, et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet. 2011;43:1022–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wiesner T, Obenauf AC, Murali R, Fried I, Griewank KG, Ulz P, et al. Germline mutations in BAP1 predispose to melanocytic tumors. Nat Genet. 2011;43:1018–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chau C, van Doorn R, van Poppelen NM, van der Stoep N, Mensenkamp AR, Sijmons RH, et al. Families with BAP1-Tumor predisposition syndrome in the netherlands: path to identification and a proposal for genetic screening guidelines. Cancers. 2019;11:1114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kadariya Y, Cheung M, Xu J, Pei J, Sementino E, Menges CW, et al. Bap1 Is a bona fide tumor suppressor: genetic evidence from mouse models carrying heterozygous germline Bap1 mutations. Cancer Res. 2016;76:2836–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Hartlerode AJ, Scully R. Mechanisms of double-strand break repair in somatic mammalian cells. Biochem J. 2009;423:157–68.

    Article  CAS  PubMed  Google Scholar 

  11. Cary RB, Peterson SR, Wang J, Bear DG, Bradbury EM, Chen DJ. DNA looping by Ku and the DNA-dependent protein kinase. Proc Natl Acad Sci USA. 1997;94:4267–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Walker JR, Corpina RA, Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 2001;412:607–14.

    Article  CAS  PubMed  Google Scholar 

  13. Yaneva M, Kowalewski T, Lieber MR. Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies. EMBO J. 1997;16:5098–112.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mahaney BL, Meek K, Lees-Miller SP. Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining. Biochem J. 2009;417:639–50.

    Article  CAS  PubMed  Google Scholar 

  15. Blunt T, Finnie NJ, Taccioli GE, Smith GC, Demengeot J, Gottlieb TM, et al. Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation. Cell. 1995;80:813–23.

    Article  CAS  PubMed  Google Scholar 

  16. Douglas P, Sapkota GP, Morrice N, Yu Y, Goodarzi AA, Merkle D, et al. Identification of in vitro and in vivo phosphorylation sites in the catalytic subunit of the DNA-dependent protein kinase. Biochem J. 2002;368:243–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Ismail IH, Davidson R, Gagne JP, Xu ZZ, Poirier GG, Hendzel MJ. Germline mutations in BAP1 impair its function in DNA double-strand break repair. Cancer Res. 2014;74:4282–94.

    Article  CAS  PubMed  Google Scholar 

  18. Kwon J, Lee D, Lee SA. BAP1 as a guardian of genome stability: implications in human cancer. Exp Mol Med. 2023;55:745–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yu H, Pak H, Hammond-Martel I, Ghram M, Rodrigue A, Daou S, et al. Tumor suppressor and deubiquitinase BAP1 promotes DNA double-strand break repair. Proc Natl Acad Sci USA. 2014;111:285–90.

    Article  CAS  PubMed  Google Scholar 

  20. Rathkey D, Khanal M, Murai J, Zhang J, Sengupta M, Jiang Q, et al. Sensitivity of mesothelioma cells to PARP inhibitors is not dependent on BAP1 but Is enhanced by temozolomide in cells with high-schlafen 11 and Low-O6-methylguanine-DNA methyltransferase expression. J Thorac Oncol. 2020;15:843–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Yang H, Xu D, Gao Y, Schmid RA, Peng RW. The association of BAP1 loss-of-function with the defect in homologous recombination repair and sensitivity to PARP-targeted therapy. J Thorac Oncol. 2020;15:e88–e90.

    Article  CAS  PubMed  Google Scholar 

  22. Fennell DA, King A, Mohammed S, Branson A, Brookes C, Darlison L, et al. Rucaparib in patients with BAP1-deficient or BRCA1-deficient mesothelioma (MiST1): an open-label, single-arm, phase 2a clinical trial. Lancet Respir Med. 2021;9:593–600.

    Article  CAS  PubMed  Google Scholar 

  23. Ghafoor A, Mian I, Wagner C, Mallory Y, Agra MG, Morrow B, et al. Phase 2 study of olaparib in malignant mesothelioma and correlation of efficacy with germline or somatic mutations in BAP1 gene. JTO Clin Res Rep. 2021;2:100231.

    PubMed  PubMed Central  Google Scholar 

  24. Passiglia F, Righi L, Bironzo P, Listì A, Farinea G, Capelletto E, et al. Niraparib plus dostarlimab in pleural mesothelioma or non-small cell lung cancer harboring HRR mutations: Interim results of the UNITO-001 phase 2 prospective trial. Clin Cancer Res. 2023. https://doi.org/10.1158/1078-0432.CCR-23-2431.

  25. Westphalen CB, Fine AD, Andre F, Ganesan S, Heinemann V, Rouleau E, et al. Pan-cancer analysis of homologous recombination repair-associated gene alterations and genome-wide loss-of-heterozygosity score. Clin Cancer Res. 2022;28:1412–21.

    Article  CAS  PubMed  Google Scholar 

  26. Baas R, JvdW F, Bleijerveld OB, van Attikum H, Sixma TK. Proteomic analysis identifies novel binding partners of BAP1. PLoS ONE. 2021;16:e0257688.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Singh A, Busacca S, Gaba A, Sheaff M, Poile C, Nakas A, et al. BAP1 loss induces mitotic defects in mesothelioma cells through BRCA1-dependent and independent mechanisms. Oncogene. 2023;42:572–85.

    Article  CAS  PubMed  Google Scholar 

  28. Masoomian B, Shields JA, Shields CL. Overview of BAP1 cancer predisposition syndrome and the relationship to uveal melanoma. J Curr Ophthalmol. 2018;30:102–9.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Eletr ZM, Yin L, Wilkinson KD. BAP1 is phosphorylated at serine 592 in S-phase following DNA damage. FEBS Lett. 2013;587:3906–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Moll U, Lau R, Sypes MA, Gupta MM, Anderson CW. DNA-PK, the DNA-activated protein kinase, is differentially expressed in normal and malignant human tissues. Oncogene. 1999;18:3114–26.

    Article  CAS  PubMed  Google Scholar 

  31. Iliakis G, Rosidi B, Wang M, Wang H. Plasmid-based assays for DNA end-joining in vitro. Methods Mol Biol. 2006;314:123–31.

    Article  CAS  PubMed  Google Scholar 

  32. Ma Y, Lieber MR. In vitro nonhomologous DNA end joining system. Methods Enzymol. 2006;408:502–10.

    Article  CAS  PubMed  Google Scholar 

  33. Zenke FT, Zimmermann A, Sirrenberg C, Dahmen H, Kirkin V, Pehl U, et al. Pharmacologic inhibitor of DNA-PK, M3814, potentiates radiotherapy and regresses human tumors in mouse models. Mol Cancer Ther. 2020;19:1091–101.

    Article  CAS  PubMed  Google Scholar 

  34. Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, et al. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet. 2016;48:407–16.

    Article  CAS  PubMed  Google Scholar 

  35. Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, et al. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. J Proteome Res. 2008;7:1346–51.

    Article  CAS  PubMed  Google Scholar 

  36. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006;127:635–48.

    Article  CAS  PubMed  Google Scholar 

  37. Serakinci N, Christensen R, Graakjaer J, Cairney CJ, Keith WN, Alsner J, et al. Ectopically hTERT expressing adult human mesenchymal stem cells are less radiosensitive than their telomerase negative counterpart. Exp Cell Res. 2007;313:1056–67.

    Article  CAS  PubMed  Google Scholar 

  38. Guo G, Chmielecki J, Goparaju C, Heguy A, Dolgalev I, Carbone M, et al. Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma. Cancer Res. 2015;75:264–9.

    Article  CAS  PubMed  Google Scholar 

  39. Zauderer MG, Bott M, McMillan R, Sima CS, Rusch V, Krug LM, et al. Clinical characteristics of patients with malignant pleural mesothelioma harboring somatic BAP1 mutations. J Thorac Oncol. 2013;8:1430–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Dogrusoz M, Ruschel Trasel A, Cao J, Ҫolak S, van Pelt SI, Kroes WGM, et al. Differential expression of DNA repair genes in prognostically-favorable versus unfavorable uveal melanoma. Cancers. 2019;11:1104.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Kuznetsoff JN, Owens DA, Lopez A, Rodriguez DA, Chee NT, Kurtenbach S, et al. Dual screen for efficacy and toxicity identifies HDAC inhibitor with distinctive activity spectrum for BAP1-mutant uveal melanoma. Mol Cancer Res. 2021;19:215–22.

    Article  CAS  PubMed  Google Scholar 

  42. Liu Z, Lin D, Zhou Y, Zhang L, Yang C, Guo B, et al. Exploring synthetic lethal network for the precision treatment of clear cell renal cell carcinoma. Sci Rep. 2022;12:13222.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Krug LM, Pass HI, Rusch VW, Kindler HL, Sugarbaker DJ, Rosenzweig KE, et al. Multicenter phase II trial of neoadjuvant pemetrexed plus cisplatin followed by extrapleural pneumonectomy and radiation for malignant pleural mesothelioma. J Clin Oncol. 2009;27:3007–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Minatel E, Trovo M, Polesel J, Baresic T, Bearz A, Franchin G, et al. Radical pleurectomy/decortication followed by high dose of radiation therapy for malignant pleural mesothelioma. Final results with long-term follow-up. Lung Cancer. 2014;83:78–82.

    Article  PubMed  Google Scholar 

  45. Boons CC, Vant MW, Burgers JA, Beckeringh JJ, Wagner C, Hugtenburg JG. The value of pemetrexed for the treatment of malignant pleural mesothelioma: a comprehensive review. Anticancer Res. 2013;33:3553–61.

    CAS  PubMed  Google Scholar 

  46. Ewald B, Sampath D, Plunkett W. H2AX phosphorylation marks gemcitabine-induced stalled replication forks and their collapse upon S-phase checkpoint abrogation. Mol Cancer Ther. 2007;6:1239–48.

    Article  CAS  PubMed  Google Scholar 

  47. Lawrence TS, Eisbruch A, McGinn CJ, Fields MT, Shewach DS. Radiosensitization by gemcitabine. Oncology. 1999;13:55–60.

    CAS  PubMed  Google Scholar 

  48. Wachters FM, van Putten JW, Maring JG, Zdzienicka MZ, Groen HJ, Kampinga HH. Selective targeting of homologous DNA recombination repair by gemcitabine. Int J Radiat Oncol Biol Phys. 2003;57:553–62.

    Article  CAS  PubMed  Google Scholar 

  49. Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol Cell. 2017;66:801–17.

    Article  CAS  PubMed  Google Scholar 

  50. Yap TA, Aerts JG, Popat S, Fennell DA. Novel insights into mesothelioma biology and implications for therapy. Nat Rev Cancer. 2017;17:475–88.

    Article  CAS  PubMed  Google Scholar 

  51. Li H, Vogel H, Holcomb VB, Gu Y, Hasty P. Deletion of Ku70, Ku80, or both causes early aging without substantially increased cancer. Mol Cell Biol. 2007;27:8205–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Righi L, Duregon E, Vatrano S, Izzo S, Giorcelli J, Rondon-Lagos M, et al. BRCA1-Associated Protein 1 (BAP1) immunohistochemical expression as a diagnostic tool in malignant pleural mesothelioma classification: a large retrospective study. J Thorac Oncol. 2016;11:2006–17.

    Article  PubMed  Google Scholar 

  53. Sebastiaan Winkler G, Lacomis L, Philip J, Erdjument-Bromage H, Svejstrup JQ, Tempst P. Isolation and mass spectrometry of transcription factor complexes. Methods. 2002;26:260–9.

    Article  CAS  PubMed  Google Scholar 

  54. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003;75:4646–58.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We are grateful to Ronald C. Hendrickson (Proteomics & Microchemistry, Memorial Sloan Kettering Cancer Center), Sho Fujisawa (Molecular Cytology, Memorial Sloan Kettering Cancer Center) and Toshiki Terao, Rina Nishiyama and Reiko Kondo (Okayama University, Medical School) for providing technical assistance and opportunities to discuss this work.

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  1. These authors contributed equally: Hiroki Sato, Tatsuo Ito.

Authors and Affiliations

  1. Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Hiroki Sato, Tatsuo Ito, Takuo Hayashi & Marc Ladanyi

  2. Department of Hygiene, Kawasaki Medical University, Okayama, Japan

    Tatsuo Ito

  3. Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Shigehisa Kitano

  4. Kimmel Center for Biology and Medicine at Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA

    Hediye Erdjument-Bromage

  5. Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Matthew J. Bott

  6. Department of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan

    Shinichi Toyooka

  7. Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Marjorie Zauderer

  8. Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Marc Ladanyi

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Contributions

TI and ML conceptualized the project. TI designed the experiments. TI and TH performed experiments. HEB helped with proteomics studies. MJB provided data. SK and ST provided advice and guidance. MGZ provided clinical context. HS and ML finalized the manuscript. ML provided overall supervision of the project.

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Correspondence to Marc Ladanyi.

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Sato, H., Ito, T., Hayashi, T. et al. The BAP1 nuclear deubiquitinase is involved in the nonhomologous end-joining pathway of double-strand DNA repair through interaction with DNA-PK. Oncogene 43, 1087–1097 (2024). https://doi.org/10.1038/s41388-024-02966-w

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