Abstract
The mutagenic APOBEC3B (A3B) cytosine deaminase is frequently over-expressed in cancer and promotes tumour heterogeneity and therapy resistance. Hence, understanding the mechanisms that underlie A3B over-expression is important, especially for developing therapeutic approaches to reducing A3B levels, and consequently limiting cancer mutagenesis. We previously demonstrated that A3B is repressed by p53 and p53 mutation increases A3B expression. Here, we investigate A3B expression upon treatment with chemotherapeutic drugs that activate p53, including 5-fluorouracil, etoposide and cisplatin. Contrary to expectation, these drugs induced A3B expression and concomitant cellular cytosine deaminase activity. A3B induction was p53-independent, as chemotherapy drugs stimulated A3B expression in p53 mutant cells. These drugs commonly activate ATM, ATR and DNA-PKcs. Using specific inhibitors and gene knockdowns, we show that activation of DNA-PKcs and ATM by chemotherapeutic drugs promotes NF-κB activity, with consequent recruitment of NF-κB to the A3B gene promoter to drive A3B expression. Further, we find that A3B knockdown re-sensitises resistant cells to cisplatin, and A3B knockout enhances sensitivity to chemotherapy drugs. Our data highlight a role for A3B in resistance to chemotherapy and indicate that stimulation of A3B expression by activation of DNA repair and NF-κB pathways could promote cancer mutations and expedite chemoresistance.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 50 print issues and online access
$259.00 per year
only $5.18 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Salter JD, Bennett RP, Smith HC. The APOBEC protein family: united by structure, divergent in function. Trends Biochem Sci. 2016;41:578–94.
Venkatesan S, Rosenthal R, Kanu N, McGranahan N, Bartek J, Quezada SA, et al. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Ann Oncol. 2018;29:563–72.
Nowarski R, Wilner OI, Cheshin O, Shahar OD, Kenig E, Baraz L, et al. APOBEC3G enhances lymphoma cell radioresistance by promoting cytidine deaminase-dependent DNA repair. Blood. 2012;120:366–75.
Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, et al. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. Elife. 2013;2:e00534.
Burns MB, Temiz NA, Harris RS. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat Genet. 2013;45:977–83.
McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med. 2015;7:283ra254.
Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013;45:970–6.
Burns MB, Lackey L, Carpenter MA, Rathore A, Land AM, Leonard B, et al. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature. 2013;494:366–70.
de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014;346:251–6.
Poulos RC, Wong YT, Ryan R, Pang H, Wong JWH. Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations. PLoS Genet. 2018;14:e1007779.
Roper N, Gao S, Maity TK, Banday AR, Zhang X, Venugopalan A, et al. APOBEC mutagenesis and copy-number alterations are drivers of proteogenomic tumor evolution and heterogeneity in metastatic thoracic tumors. Cell Rep. 2019;26:2651–66. e2656.
Law EK, Sieuwerts AM, LaPara K, Leonard B, Starrett GJ, Molan AM, et al. The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer. Sci Adv. 2016;2:e1601737.
Schmitt C, Lucius R, Synowitz M, Held-Feindt J, Hattermann K. APOBEC3B is expressed in human glioma, and influences cell proliferation and temozolomide resistance. Oncol Rep. 2018;40:2742–9.
Refsland EW, Stenglein MD, Shindo K, Albin JS, Brown WL, Harris RS. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res. 2010;38:4274–84.
Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, et al. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res. 2017;45:11056–69.
Periyasamy M, Patel H, Lai CF, Nguyen VTM, Nevedomskaya E, Harrod A, et al. APOBEC3B-mediated cytidine deamination is required for estrogen receptor action in breast cancer. Cell Rep. 2015;13:108–21.
Menendez D, Nguyen TA, Snipe J, Resnick MA. The cytidine deaminase APOBEC3 family is subject to transcriptional regulation by p53. Mol cancer Res: MCR. 2017;15:735–43.
Vassilev LT, Tovar C, Chen S, Knezevic D, Zhao X, Sun H, et al. Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc Natl Acad Sci USA. 2006;103:10660–5.
Andrysik Z, Galbraith MD, Guarnieri AL, Zaccara S, Sullivan KD, Pandey A, et al. Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity. Genome Res. 2017;27:1645–57.
Green AM, Weitzman MD. The spectrum of APOBEC3 activity: from anti-viral agents to anti-cancer opportunities. DNA Repair. 2019;83:102700.
Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol. 2010;17:222–9.
McDaniel YZ, Wang D, Love RP, Adolph MB, Mohammadzadeh N, Chelico L, et al. Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure. Nucleic Acids Res. 2020;48:1353–71.
Kubo K, Ide H, Wallace SS, Kow YW. A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion. Biochemistry. 1992;31:3703–8.
Wyatt MD, Wilson DM 3rd. Participation of DNA repair in the response to 5-fluorouracil. Cell Mol Life Sci. 2009;66:788–99.
Wilson DM 3rd, Seidman MM. A novel link to base excision repair? Trends Biochem Sci. 2010;35:247–52.
Pommier Y, Huang SY, Gao R, Das BB, Murai J, Marchand C. Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2). DNA Repair. 2014;19:114–29.
Beshiri ML, Holmes KB, Richter WF, Hess S, Islam AB, Yan Q, et al. Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. Proc Natl Acad Sci USA. 2012;109:18499–504.
Leonard B, McCann JL, Starrett GJ, Kosyakovsky L, Luengas EM, Molan AM, et al. The PKC/NF-kappaB signaling pathway induces APOBEC3B expression in multiple human cancers. Cancer Res. 2015;75:4538–47.
Maruyama W, Shirakawa K, Matsui H, Matsumoto T, Yamazaki H, Sarca AD, et al. Classical NF-kappaB pathway is responsible for APOBEC3B expression in cancer cells. Biochem Biophys Res Commun. 2016;478:1466–71.
Strickson S, Campbell DG, Emmerich CH, Knebel A, Plater L, Ritorto MS, et al. The anti-inflammatory drug BAY 11-7082 suppresses the MyD88-dependent signalling network by targeting the ubiquitin system. Biochem J. 2013;451:427–37.
Podolin PL, Callahan JF, Bolognese BJ, Li YH, Carlson K, Davis TG, et al. Attenuation of murine collagen-induced arthritis by a novel, potent, selective small molecule inhibitor of IkappaB Kinase 2, TPCA-1 (2-[(aminocarbonyl)amino]-5-(4-fluorophenyl)-3-thiophenecarboxamide), occurs via reduction of proinflammatory cytokines and antigen-induced T cell proliferation. J Pharm Exp Ther. 2005;312:373–81.
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.
Hadian K, Krappmann D. Signals from the nucleus: activation of NF-kappaB by cytosolic ATM in the DNA damage response. Sci Signal. 2011;4:pe2.
Liu L, Kwak YT, Bex F, Garcia-Martinez LF, Li XH, Meek K, et al. DNA-dependent protein kinase phosphorylation of IkappaB alpha and IkappaB beta regulates NF-kappaB DNA binding properties. Mol Cell Biol. 1998;18:4221–34.
Bozulic L, Surucu B, Hynx D, Hemmings BA. PKBalpha/Akt1 acts downstream of DNA-PK in the DNA double-strand break response and promotes survival. Mol Cell. 2008;30:203–13.
Oeckinghaus A, Hayden MS, Ghosh S. Crosstalk in NF-kappaB signaling pathways. Nat Immunol. 2011;12:695–708.
Gavande NS, VanderVere-Carozza PS, Hinshaw HD, Jalal SI, Sears CR, Pawelczak KS, et al. DNA repair targeted therapy: The past or future of cancer treatment? Pharm Ther. 2016;160:65–83.
Peng Y, Woods RG, Beamish H, Ye R, Lees-Miller SP, Lavin MF, et al. Deficiency in the catalytic subunit of DNA-dependent protein kinase causes down-regulation of ATM. Cancer Res. 2005;65:1670–7.
Hong SP, Chan TE, Lombardo Y, Corleone G, Rotmensz N, Bravaccini S, et al. Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. Nat Commun. 2019;10:3840.
Gadducci A, Guarneri V, Peccatori FA, Ronzino G, Scandurra G, Zamagni C, et al. Current strategies for the targeted treatment of high-grade serous epithelial ovarian cancer and relevance of BRCA mutational status. J Ovarian Res. 2019;12:9.
Stronach EA, Chen M, Maginn EN, Agarwal R, Mills GB, Wasan H, et al. DNA-PK mediates AKT activation and apoptosis inhibition in clinically acquired platinum resistance. Neoplasia. 2011;13:1069–80.
Langdon SP, Lawrie SS, Hay FG, Hawkes MM, McDonald A, Hayward IP, et al. Characterization and properties of nine human ovarian adenocarcinoma cell lines. Cancer Res. 1988;48:6166–72.
Basu S, Rosenzweig KR, Youmell M, Price BD. The DNA-dependent protein kinase participates in the activation of NF kappa B following DNA damage. Biochem Biophys Res Commun. 1998;247:79–83.
Panta GR, Kaur S, Cavin LG, Cortes ML, Mercurio F, Lothstein L, et al. ATM and the catalytic subunit of DNA-dependent protein kinase activate NF-kappaB through a common MEK/extracellular signal-regulated kinase/p90(rsk) signaling pathway in response to distinct forms of DNA damage. Mol Cell Biol. 2004;24:1823–35.
Sabatel H, Pirlot C, Piette J, Habraken Y. Importance of PIKKs in NF-kappaB activation by genotoxic stress. Biochem Pharm. 2011;82:1371–83.
Fang Y, Chai Z, Wang D, Kuang T, Wu W, Lou W. DNA-PKcs deficiency sensitizes the human hepatoma HepG2 cells to cisplatin and 5-fluorouracil through suppression of the PI3K/Akt/NF-kappaB pathway. Mol Cell Biochem. 2015;399:269–78.
Rajagopalan S, Moyle MW, Joosten I, Long EO. DNA-PKcs controls an endosomal signaling pathway for a proinflammatory response by natural killer cells. Sci Signal. 2010;3:ra14.
Faltas BM, Prandi D, Tagawa ST, Molina AM, Nanus DM, Sternberg C, et al. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nat Genet. 2016;48:1490–9.
Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, et al. Tracking the evolution of non-small-cell lung cancer. N Engl J Med. 2017;376:2109–21.
Treiber T, Treiber N, Plessmann U, Harlander S, Daiss JL, Eichner N, et al. A compendium of RNA-binding proteins that regulate microRNA biogenesis. Mol Cell. 2017;66:270–84. e213.
Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP, Bolli N, et al. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat Genet. 2014;46:487–91.
Zaky A, Busso C, Izumi T, Chattopadhyay R, Bassiouny A, Mitra S, et al. Regulation of the human AP-endonuclease (APE1/Ref-1) expression by the tumor suppressor p53 in response to DNA damage. Nucleic Acids Res. 2008;36:1555–66.
Serebrenik AA, Argyris PP, Jarvis MC, Brown WL, Bazzaro M, Vogel RI, et al. The DNA cytosine deaminase APOBEC3B is a molecular determinant of platinum responsiveness in clear cell ovarian cancer. Clin Cancer Res: Off J Am Assoc Cancer Res. 2020;26:3397–407.
Leonard B, Starrett GJ, Maurer MJ, Oberg AL, Van Bockstal M, Van, et al. APOBEC3G expression correlates with T-cell infiltration and improved clinical outcomes in high-grade serous ovarian carcinoma. Clin Cancer Res: Off J Am Assoc Cancer Res. 2016;22:4746–55.
Sur S, Pagliarini R, Bunz F, Rago C, Diaz LA Jr., Kinzler KW, et al. A panel of isogenic human cancer cells suggests a therapeutic approach for cancers with inactivated p53. Proc Natl Acad Sci USA. 2009;106:3964–9.
Ding Q, Regan SN, Xia Y, Oostrom LA, Cowan CA, Musunuru K. Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell. 2013;12:393–4.
Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486:346–52.
Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9:671–5.
Acknowledgements
We thank Dr B Vogelstein for p53-null HCT116 cells. We are grateful to Dr S Langdon for the PEA1 and PEA2 lines. Our thanks also go to Drs. S Hong and L Magnani for their kind gift of PEOO3 cells. This study was supported by Cancer Research UK grant C37/A18784. We thank the LMS/NIHR Imperial Biomedical Research Centre Flow Cytometry Facility for support. Additional support was provided by the Imperial Experimental Cancer Medicine Centre, Imperial NIHR Biomedical Research Centre, and the Cancer Research UK Imperial Centre. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
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
About this article
Cite this article
Periyasamy, M., Singh, A.K., Gemma, C. et al. Induction of APOBEC3B expression by chemotherapy drugs is mediated by DNA-PK-directed activation of NF-κB. Oncogene 40, 1077–1090 (2021). https://doi.org/10.1038/s41388-020-01583-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41388-020-01583-7
This article is cited by
-
APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential
Journal of Hematology & Oncology (2023)
-
Addressing the benefits of inhibiting APOBEC3-dependent mutagenesis in cancer
Nature Genetics (2022)
-
Cardamonin inhibits the expression of P-glycoprotein and enhances the anti-proliferation of paclitaxel on SKOV3-Taxol cells
Journal of Natural Medicines (2022)
-
Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways
Nature Communications (2021)
-
Coregulation of pathways in lung cancer patients with EGFR mutation: therapeutic opportunities
British Journal of Cancer (2021)