Abstract
In response to genotoxic stress, multiple kinase signaling cascades are activated, many of them directed towards the tumor suppressor p53, which coordinates the DNA damage response (DDR). Defects in DDR pathways lead to an accumulation of mutations that can promote tumorigenesis. Emerging evidence implicates multiple members of the NimA-related kinase (NEK) family (NEK1, NEK10, and NEK11) in the DDR. Here, we describe a function for NEK10 in the regulation of p53 transcriptional activity through tyrosine phosphorylation. NEK10 loss increases cellular proliferation by modulating the p53-dependent transcriptional output. NEK10 directly phosphorylates p53 on Y327, revealing NEK10’s unexpected substrate specificity. A p53 mutant at this site (Y327F) acts as a hypomorph, causing an attenuated p53-mediated transcriptional response. Consistently, NEK10-deficient cells display heightened sensitivity to DNA-damaging agents. Further, a combinatorial score of NEK10 and TP53-target gene expression is an independent predictor of a favorable outcome in breast cancers.
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
Menendez D, Inga A, Resnick MA. The expanding universe of p53 targets. Nat Rev Cancer. 2009;9:724–37.
Kastenhuber ER, Lowe SW. Putting p53 in context. Cell. 2017;170:1062–78.
Horn HF, Vousden KH. Coping with stress: multiple ways to activate p53. Oncogene. 2007;26:1306–16.
Pappas K, Xu J, Zairis S, Resnick-Silverman L, Abate F, Steinbach N. et al. p53 maintains baseline expression of multiple tumor suppressor genes. Mol Cancer Res. 2017;15:1051–62.
McGranahan N, Swanton C. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell. 2017;168:613–28.
Malkin D. Li-fraumeni syndrome. Genes Cancer. 2011;2:475–84.
Riley T, Sontag E, Chen P, Levine A. Transcriptional control of human p53-regulated genes. Nat Rev Mol Cell Biol. 2008;9:402–12.
Huang LC, Clarkin KC, Wahl GM. Sensitivity and selectivity of the DNA damage sensor responsible for activating p53-dependent G1 arrest. Proc Natl Acad Sci USA. 1996;93:4827–32.
Kumari R, Kohli S, Das S. p53 regulation upon genotoxic stress: intricacies and complexities. Mol Cell Oncol. 2014;1:e969653.
Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol. 2019;20:199–210.
Chen Y, Chen PL, Chen CF, Jiang X, Riley DJ. Never-in-mitosis related kinase 1 functions in DNA damage response and checkpoint control. Cell Cycle. 2008;7:3194–201.
Chen Y, Chen CF, Riley DJ, Chen PL. Nek1 kinase functions in DNA damage response and checkpoint control through a pathway independent of ATM and ATR. Cell Cycle. 2011;10:655–63.
Sabir SR, Sahota NK, Jones GD, Fry AM. Loss of Nek11 prevents G2/M arrest and promotes cell death in HCT116 colorectal cancer cells exposed to therapeutic DNA damaging agents. PLoS ONE. 2015;10:e0140975
Melixetian M, Klein DK, Sorensen CS, Helin K. NEK1 regulates CDC25A degradation and the IR-induced G2/M checkpoint. Nat Cell Biol. 2009;11:1247–53.
Noguchi K, Fukazawa H, Murakami Y, Uehara Y. Nek1 a new member of the NIMA family of kinases, involved in DNA replication and genotoxic stress responses. J Biol Chem. 2002;277:39655–65.
Fletcher L, Cerniglia GJ, Nigg EA, Yend TJ, Muschel RJ. Inhibition of centrosome separation after DNA damage: a role for Nek2. Radiat Res. 2004;162:128–35.
Mi J, Guo C, Brautigan DL, Larner JM. Protein phosphatase-1alpha regulates centrosome splitting through Nek2. Cancer Res. 2007;67:1082–9.
Lee M.Y, Kim H.J, Kim M.A, Jee H.J, Kim A.J, Bae Y.S. et al. Nek6 is involved in G2/M phase cell cycle arrest through DNA damage-induced phosphorylation. Cell Cycle. 2008;7:2705–9.
Choi HJ, Lin JR, Vannier JB, Slaats GG, Kile AC, Paulsen RD. et al. NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies. Mol Cell. 2013;51:423–39.
Abeyta A, Castella M, Jacquemont C, Taniguchi T. NEK8 regulates DNA damage-induced RAD51 foci formation and replication fork protection. Cell Cycle. 2017;16:335–47.
Smith SC, Petrova AV, Madden MZ, Wang H, Pan Y, Warren MD. et al. A gemcitabine sensitivity screen identifies a role for NEK9 in the replication stress response. Nucleic Acids Res. 2014;42:11517–27.
Moniz LS, Stambolic V. Nek10 mediates G2/M cell cycle arrest and MEK autoactivation in response to UV irradiation. Mol Cell Biol. 2011;31:30–42.
Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017;45:D777–83.
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO. et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6:pp 11
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Disco. 2012;2:401–4.
Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA. Cancer Genome Atlas Research, N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113–20.
Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, Platte R. et al. Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nat Genet. 2009;41:585–90.
Cazzalini O, Scovassi AI, Savio M, Stivala LA, Prosperi E. Multiple roles of the cell cycle inhibitor p21(CDKN1A) in the DNA damage response. Mutat Res. 2010;704:12–20.
Besson A, Dowdy SF, Roberts JM. CDK inhibitors: cell cycle regulators and beyond. Dev Cell. 2008;14:159–69.
Giono LE, Manfredi JJ. The p53 tumor suppressor participates in multiple cell cycle checkpoints. J Cell Physiol. 2006;209:13–20.
Junttila MR, Evan GI. p53-a Jack of all trades but master of none. Nat Rev Cancer. 2009;9:821–9.
Moniz, LS. Characterization of NimA-related kinase 10 (NEK10): a role in checkpoint control. University of Toronto, Toronto, Canada; 2010. 178 leaves.
Huang YF, Bulavin DV. Oncogene-mediated regulation of p53 ISGylation and functions. Oncotarget. 2014;5:5808–18.
Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY. et al. Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. Nat Commun. 2015;6:6622
Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M. et al. Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Cancer Res. 2012;72:2501–11.
van de Kooij B, Creixell P, van Vlimmeren A, Joughin B, Miller CJ, Haider N. et al. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. Elife. 2019;8:e44635. https://doi.org/10.7554/eLife.44635.
Kawaguchi T, Kato S, Otsuka K, Watanabe G, Kumabe T, Tominaga T. et al. The relationship among p53 oligomer formation, structure and transcriptional activity using a comprehensive missense mutation library. Oncogene. 2005;24:6976–81.
Yakovlev VA, Bayden AS, Graves PR, Kellogg GE, Mikkelsen RB. Nitration of the tumor suppressor protein p53 at tyrosine 327 promotes p53 oligomerization and activation. Biochemistry. 2010;49:5331–9.
Chong LT, Swope WC, Pitera JW, Pande VS. Kinetic computational alanine scanning: application to p53 oligomerization. J Mol Biol. 2006;357:1039–49.
Davies H, Hunter C, Smith R, Stephens P, Greenman C, Bignell G. et al. Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res. 2005;65:7591–5.
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G. et al. Patterns of somatic mutation in human cancer genomes. Nature. 2007;446:153–8.
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.
Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD. et al. An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell. 2018;173:400–416 e11.
Fischer M. Census and evaluation of p53 target genes. Oncogene. 2017;36:3943–56.
McGale P, Taylor C, Correa C, Cutter D, Duane F. EBCTC, G et al. Effect of radiotherapy after mastectomy and axillary surgery on 10-year recurrence and 20-year breast cancer mortality: meta-analysis of individual patient data for 8135 women in 22 randomised trials. Lancet. 2014;383:2127–35.
Darby S, McGale P, Correa C, Taylor C, Arriagada R. Early Breast Cancer Trialists’ Collaborative, G. et al. Effect of radiotherapy after breast-conserving surgery on 10-year recurrence and 15-year breast cancer death: meta-analysis of individual patient data for 10,801 women in 17 randomised trials. Lancet. 2011;378:1707–16.
Lakin ND, Jackson SP. Regulation of p53 in response to DNA damage. Oncogene. 1999;18:7644–55.
Meek DW. The p53 response to DNA damage. DNA Repair (Amst). 2004;3:1049–56.
Jee HJ, Kim AJ, Song N, Kim HJ, Kim M, Koh Ne H. et al. k6 overexpression antagonizes p53-induced senescence in human cancer cells. Cell Cycle. 2010;9:4703–10.
Salem H, Rachmin I, Yissachar N, Cohen S, Amiel A, Haffner R. et al. Nek7 kinase targeting leads to early mortality, cytokinesis disturbance and polyploidy. Oncogene. 2010;29:4046–57.
Moniz L, Dutt P, Haider N, Stambolic V. Nek family of kinases in cell cycle, checkpoint control and cancer. Cell Div. 2011;6:18
Wang S, El-Deiry WS. p73 or p53 directly regulates human p53 transcription to maintain cell cycle checkpoints. Cancer Res. 2006;66:6982–9.
Hudson JM, Frade R, Bar-Eli M. Wild-type p53 regulates its own transcription in a cell-type specific manner. DNA Cell Biol. 1995;14:759–66.
Deffie A, Wu H, Reinke V, Lozano G. The tumor suppressor p53 regulates its own transcription. Mol Cell Biol. 1993;13:3415–23.
Jin S, Tong T, Fan W, Fan F, Antinore MJ, Zhu X. et al. GADD45-induced cell cycle G2-M arrest associates with altered subcellular distribution of cyclin B1 and is independent of p38 kinase activity. Oncogene. 2002;21:8696–704.
Wang XW, Zhan Q, Coursen JD, Khan MA, Kontny HU, Yu L. et al. GADD45 induction of a G2/M cell cycle checkpoint. Proc Natl Acad Sci USA. 1999;96:3706–11.
Taylor WR, Stark GR. Regulation of the G2/M transition by p53. Oncogene. 2001;20:1803–15.
Liu L, Scolnick DM, Trievel RC, Zhang HB, Marmorstein R, Halazonetis TD. et al. p53 sites acetylated in vitro by PCAF and p300 are acetylated in vivo in response to DNA damage. Mol Cell Biol. 1999;19:1202–9.
Knights CD, Catania J, Di Giovanni S, Muratoglu S, Perez R, Swartzbeck A. et al. Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate. J Cell Biol. 2006;173:533–44.
Chao C, Wu Z, Mazur SJ, Borges H, Rossi M, Lin T. et al. Acetylation of mouse p53 at lysine 317 negatively regulates p53 apoptotic activities after DNA damage. Mol Cell Biol. 2006;26:6859–69.
Lord CJ, Ashworth A. BRCAness revisited. Nat Rev Cancer. 2016;16:110–20.
Tutt A, Tovey H, Cheang MCU, Kernaghan S, Kilburn L, Gazinska P. et al. Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial. Nat Med. 2018;24:628–37.
Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:395–9.
Burstein MD, Tsimelzon A, Poage GM, Covington KR, Contreras A, Fuqua SA. et al. Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer. Clin Cancer Res. 2015;21:1688–98.
Vichai V, Kirtikara K. Sulforhodamine B colorimetric assay for cytotoxicity screening. Nat Protoc. 2006;1:1112–6.
Franken NA, Rodermond HM, Stap J, Haveman J, van Bree C. et al. Clonogenic assay of cells in vitro. Nat Protoc.2006;1:2315–9.
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3:1101–8.
Salic A, Mitchison TJ. A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc Natl Acad Sci USA. 2008;105:2415–20.
Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y. Cancer Genome Atlas Research, N. et al. Integrated genomic characterization of endometrial carcinoma. Nature. 2013;497:67–73.
Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinforma. 2013;14:7.
Acknowledgements
We thank Ryan Dowling and members of the Stambolic group (Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada) for their helpful discussion and advice. We thank Anne van Vlimmeren for technical assistance. This work was supported by the Princess Margaret Hospital Foundation and by the CIHR strategic training fellowship of the EIRR 21st Program (Awarded to NH). The results published here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.
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
Haider, N., Dutt, P., van de Kooij, B. et al. NEK10 tyrosine phosphorylates p53 and controls its transcriptional activity. Oncogene 39, 5252–5266 (2020). https://doi.org/10.1038/s41388-020-1361-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41388-020-1361-x