An Integrative “Omics” Approach, for Identification of Bona Fides PLK1 Associated Biomarker in Esophageal Adenocarcinoma

Author(s): Nousheen Bibi*, Sajid Rashid, Judith Nicholson, Mark Malloy, Rob O'Neill, David Blake, Ted Hupp

Journal Name: Current Cancer Drug Targets

Volume 19 , Issue 9 , 2019

  Journal Home
Translate in Chinese
Become EABM
Become Reviewer

Graphical Abstract:


Abstract:

Background: The rapid expansion of genome-wide profiling techniques offers the opportunity to utilize various types of information collected in the study of human health and disease. Overexpression of Polo like kinase 1 (PLK1) is associated with esophageal adenocarcinoma (OAC), however biological functions and molecular targets of PLK1 in OAC are still unknown.

Objectives: Here we performed integrative analysis of two “omics” data sources to reveal high-level interactions of PLK1 associated with OAC.

Methods: Initially, quantitative gene expression (RPKM) was measured from transcriptomics data set of four OAC patients. In parallel, alteration in phosphorylation levels was evaluated in the proteomics data set (mass spectrometry) in OAC cell line (PLK1 inhibited). Next, two “omics” data sets were integrated and through comprehensive analysis possible true PLK1 targets that may serve as OAC biomarkers were assembled.

Results: Through experimental validation, small ubiquitin-related modifier 1 (SUMO1) and heat shock protein beta-1 (HSPB1) were identified as novel phosphorylation targets of PLK1. Consequently in vivo, in situ and in silico experiments clearly demonstrated the interaction of PLK1 with putative novel targets (SUMO1 and HSPB1).

Conclusion: Identification of a PLK1 dependent biosignature in OAC with high confidence in two omics levels proven the robustness and efficacy of our integrative approach.

Keywords: Omics, PLK1, SUMO1, HSPB1, kinase assay, ELISA, co-IP, PLA, in silico.

[1]
Elia, A.E.; Rellos, P.; Haire, L.F.; Chao, J.W.; Ivins, F.J.; Hoepker, K.; Mohammad, D.; Cantley, L.C.; Smerdon, S.J.; Yaffe, M.B. The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell, 2003, 115(1), 83-95.
[2]
Strebhardt, K.; Ullrich, A. Targeting polo-like kinase 1 for cancer therapy. Nat. Rev. Cancer, 2006, 6(4), 321-330.
[3]
Golsteyn, R.M.; Mundt, K.E.; Fry, A.M.; Nigg, E.A. Cell cycle regulation of the activity and subcellular localization of Plk1, a human protein kinase implicated in mitotic spindle function. J. Cell Biol., 1995, 129(6), 1617-1628.
[4]
Toyoshima-Morimoti, F.; Taniguchi, E.; Shinya, N.; Iwamatsu, A.; Nishida, E. erratum: Polo-like kinase 1 phosphorylates cyclin B1 and targets it to the nucleus during prophase. Nature, 2001, 410(6830), 847-847.
[5]
Lane, H.A.; Nigg, E.A. Antibody microinjection reveals an essential role for human polo-like kinase 1 (Plk1) in the functional maturation of mitotic centrosomes. J. Cell Biol., 1996, 135(6), 1701-1713.
[6]
Kops, G.J.; Weaver, B.A.; Cleveland, D.W. On the road to cancer: aneuploidy and the mitotic checkpoint. Nat. Rev. Cancer, 2005, 5(10), 773-785.
[7]
Takahashi, T.; Sano, B.; Nagata, T.; Kato, H.; Sugiyama, Y.; Kunieda, K.; Kimura, M.; Okano, Y.; Saji, S. Polo‐like kinase 1 (PLK1) is overexpressed in primary colorectal cancers. Cancer Sci., 2003, 94(2), 148-152.
[8]
Wolf, G.; Hildenbrand, R.; Schwar, C.; Grobholz, R.; Kaufmann, M.; Stutte, H-J.; Strebhardt, K.; Bleyl, U. Polo-like kinase: a novel marker of proliferation: correlation with estrogen-receptor expression in human breast cancer. Pathol. Res. Pract., 2000, 196(11), 753-759.
[9]
Tokumitsu, Y.; Mori, M.; Tanaka, S.; Akazawa, K.; Nakano, S.; Niho, Y. Prognostic significance of polo-like kinase expression in esophageal carcinoma. Int. J. Oncol., 1999, 15(4), 687-779.
[10]
Gray, P.J.; Bearss, D.J.; Han, H.; Nagle, R.; Tsao, M-S.; Dean, N.; Von Hoff, D.D. Identification of human polo-like kinase 1 as a potential therapeutic target in pancreatic cancer. Cancer Res., 2004, 3(5), 641-646.
[11]
Knecht, R.; Elez, R.; Oechler, M.; Solbach, C.; von Ilberg, C.; Strebhardt, K. Prognostic significance of polo-like kinase (PLK) expression in squamous cell carcinomas of the head and neck. Cancer Res., 1999, 59(12), 2794-2797.
[12]
Takai, N.; Miyazaki, T.; Fujisawa, K.; Nasu, K.; Hamanaka, R.; Miyakawa, I. Expression of polo-like kinase in ovarian cancer is associated with histological grade and clinical stage. Cancer Lett., 2001, 164(1), 41-49.
[13]
Sato, F.; Abraham, J.M.; Yin, J.; Kan, T.; Ito, T.; Mori, Y.; Hamilton, J.P.; Jin, Z.; Cheng, Y.; Paun, B. Polo-like kinase and survivin are esophageal tumor-specific promoters. Biochem. Biophys. Res. Commun., 2006, 342(2), 465-471.
[14]
Feng, Y.B.; Lin, D.C.; Shi, Z.Z.; Wang, X.C.; Shen, X.M.; Zhang, Y.; Du, X.L.; Luo, M.L.; Xu, X.; Han, Y.L. Overexpression of PLK1 is associated with poor survival by inhibiting apoptosis via enhancement of survivin level in esophageal squamous cell carcinoma. Int. J. Cancer, 2009, 124(3), 578-588.
[15]
Coupland, V.H.; Allum, W.; Blazeby, J.M.; Mendall, M.A.; Hardwick, R.H.; Linklater, K.M.; Møller, H.; Davies, E.A. Incidence and survival of esophageal and gastric cancer in England between 1998 and 2007, a population-based study. BMC Cancer, 2012, 12(1)
[16]
Adams, R.; Morgan, M.; Mukherjee, S.; Brewster, A.; Maughan, T.; Morrey, D.; Havard, T.; Lewis, W.; Clark, G.; Roberts, S. A prospective comparison of multidisciplinary treatment of esophageal cancer with curative intent in a UK cancer network. Eur. J. Surg. Oncol., 2007, 33(3), 307-313.
[17]
WHO. World Cancer Report; Lyon IARC Press, 2003.
[18]
Kim, S.M.; Park, Y-Y.; Park, E.S.; Cho, J.Y.; Izzo, J.G.; Zhang, D.; Kim, S-B.; Lee, J.H.; Bhutani, M.S.; Swisher, S.G. Prognostic biomarkers for esophageal adenocarcinoma identified by analysis of tumor transcriptome. PLoS One, 2010, 5(11)e15074
[19]
Peters, C.J.; Rees, J.R.; Hardwick, R.H.; Hardwick, J.S.; Vowler, S.L.; Ong, C.A.J.; Zhang, C.; Save, V.; O’Donovan, M.; Rassl, D. A 4-gene signature predicts survival of patients with resected adenocarcinoma of the esophagus, junction, and gastric cardia. Gastroenterology, 2010, 139(6), 1995-2004.
[20]
Chin, L.; Gray, J.W. Translating insights from the cancer genome into clinical practice. Nature, 2008, 452(7187), 553-563.
[21]
Hawkins, R.D.; Hon, G.C.; Ren, B. Next-generation genomics: An integrative approach. Nat. Rev. Genet., 2010, 11(7), 476-486.
[22]
Berger, J.A.; Hautaniemi, S.; Mitra, S.K.; Astola, J. Jointly analyzing gene expression and copy number data in breast cancer using data reduction models. IEEE/ACM Tr Comp. Biol. Bioinf., 2006, 3(1), 2.
[23]
Shen, R.; Olshen, A.B.; Ladanyi, M. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics, 2009, 25(22), 2906-2912.
[24]
Guex, N.; Peitsch, M.C.; Schwede, T. Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective. Electrophoresis, 2009, 30(S1)
[25]
Sheelagh, F.; Claire, A.; Robert, O.; Jonathan, H.; Stephen, T.; Ted, H.; David, B.; Daniella, Z. Potent and selective small molecule inhibitors of Polo-like kinase 1: Biological characterization AACR 103rd Annual Meeting 2012. Chicago, IL.
[26]
Wu, S.; Zhang, Y. MUSTER: improving protein sequence profile–profile alignments by using multiple sources of structure information. Proteins Structure, Function, Bioinformatics, 2008, 72(2), 547-556.
[27]
Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
[28]
De Vries, S.J.; Van Dijk, M.; Bonvin, A.M. The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc., 2010, 5(5), 883-897.
[29]
Torchala, M.; Moal, I.H.; Chaleil, R.A.; Fernandez-Recio, J.; Bates, P.A. SwarmDock: A server for flexible protein–protein docking. Bioinformatics, 2013, 29(6), 807-809.
[30]
Tovchigrechko, A.; Vakser, I.A. GRAMM-X public web server for protein–protein docking. Nucleic Acids Res., 2006, 34(suppl_2), W310-W314.
[31]
Meng, E.C.; Pettersen, E.F.; Couch, G.S.; Huang, C.C.; Ferrin, T.E. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics, 2006, 7(1), 339.
[32]
Wallace, A.C.; Laskowski, R.A.; Thornton, J.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 1995, 8(2), 127-134.
[33]
Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 2008, 5(7), 621-628.
[34]
Yaffe, M.B.; Smerdon, S.J. The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function. Annu. Rev. Biophys. Biomol. Struct., 2004, 33, 225-244.
[35]
Emsley, P.; Lohkamp, B.; Scott, W.G.; Cowtan, K. Features and development of Coot. Acta Crystallogr. D., 2010, 66(4), 486-501.
[36]
Barr, F.A.; Silljé, H.H.; Nigg, E.A. Polo-like kinases and the orchestration of cell division. Nat. Rev. Mol. Cell Biol., 2004, 5(6), 429-441.
[37]
Petronczki, M.; Lénárt, P.; Peters, J-M. Polo on the rise-from mitotic entry to cytokinesis with Plk1. Dev. Cell, 2008, 14(5), 646-659.
[38]
Archambault, V.; Glover, D.M. Polo-like kinases: conservation and divergence in their functions and regulation. Nat. Rev. Mol. Cell Biol., 2009, 10(4), 265-275.
[39]
Taylor, S.; Peters, J-M. Polo and Aurora kinases-lessons derived from chemical biology. Curr. Opin. Cell Biol., 2008, 20(1), 77-84.
[40]
Tsvetkov, L.; Stern, D.F. Interaction of chromatin-associated Plk1 and Mcm7. J. Biol. Chem., 2005, 280(12), 11943-11947.
[41]
Van Vugt, M.A.; Gardino, A.K.; Linding, R.; Ostheimer, G.J.; Reinhardt, H.C.; Ong, S-E.; Tan, C.S.; Miao, H.; Keezer, S.M.; Li, J. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G2/M DNA damage checkpoint. PLoS Biol., 2010, 8(1)e1000287
[42]
Luca, M.D.; Lavia, P.; Guarguaglini, G. A functional interplay between Aurora-A, Plk1 and TPX2 at spindle poles: Plk1 controls centrosomal localization of Aurora-A and TPX2 spindle association. Cell Cycle, 2006, 5(3), 296-303.
[43]
Li, H.; Wang, Y.; Liu, X. Plk1-dependent phosphorylation regulates functions of DNA topoisomerase IIα in cell cycle progression. J. Biol. Chem., 2008, 283(10), 6209-6221.
[44]
Denison, C.; Rudner, A.D.; Gerber, S.A.; Bakalarski, C.E.; Moazed, D.; Gygi, S.P. A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol. Cell. Proteomics, 2005, 4(3), 246-254.
[45]
Hannich, J.T.; Lewis, A.; Kroetz, M.B.; Li, S-J.; Heide, H.; Emili, A.; Hochstrasser, M. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem., 2005, 280(6), 4102-4110.
[46]
Panse, V.G.; Hardeland, U.; Werner, T.; Kuster, B.; Hurt, E. A proteome-wide approach identifies sumoylated substrate proteins in yeast. J. Biol. Chem., 2004, 279(40), 41346-41351.
[47]
Wohlschlegel, J.A.; Johnson, E.S.; Reed, S.I.; Yates, J.R. Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem., 2004, 279(44), 45662-45668.
[48]
Dasso, M. Emerging roles of the SUMO pathway in mitosis. Cell Div., 2008, 3(1), 5.
[49]
Gill, G. Something about SUMO inhibits transcription. Curr. Opin. Genet. Dev., 2005, 15(5), 536-541.
[50]
Hay, R.T. SUMO: A history of modification. Mol. Cell, 2005, 18(1), 1-12.
[51]
Hay, R. Role of ubiquitin-like proteins in transcriptional regulation. In: The Histone Code and Beyond; Springer, 2006; pp. 173-192.
[52]
Moschos, S.J.; Mo, Y-Y. Role of SUMO/Ubc9 in DNA damage repair and tumorigenesis. J. Mol. Histol., 2006, 37(5), 309-319.
[53]
Pastushok, L.; Xiao, W. DNA postreplication repair modulated by ubiquitination and sumoylation. Adv. Protein Chem., 2004, 69, 279-306.
[54]
Seeler, J-S.; Bischof, O.; Nacerddine, K.; Dejean, A. SUMO, the three Rs and cancer. In: Acute Promyelocytic Leukemia; Springer, 2007; pp. 49-71.
[55]
Matic, I.; Macek, B.; Hilger, M.; Walther, T.C.; Mann, M. Phosphorylation of SUMO-1 occurs in vivo and is conserved through evolution. J. Proteome Res., 2008, 7(9), 4050-4057.
[56]
Rodriguez, M.S.; Desterro, J.M.; Lain, S.; Midgley, C.A.; Lane, D.P.; Hay, R.T. SUMO‐1 modification activates the transcriptional response of p53. EMBO J., 1999, 18(22), 6455-6461.
[57]
McKenzie, L.; King, S.; Marcar, L.; Nicol, S.; Dias, S.S.; Schumm, K.; Robertson, P.; Bourdon, J-C.; Perkins, N.; Fuller-Pace, F. p53-dependent repression of polo-like kinase-1 (PLK1). Cell Cycle, 2010, 9(20), 4200-4212.
[58]
Zhu, H.; Chang, B-D.; Uchiumi, T.; Roninson, I.B. Identification of promoter elements responsible for transcriptional inhibition of polo-like kinase 1 and topoisomerase iiα genes by p21WAF1/ CIP1/SDI1. Cell Cycle, 2002, 1(1), 55-62.
[59]
Stamler, R.; Kappé, G.; Boelens, W.; Slingsby, C. Wrapping the α-crystallin domain fold in a chaperone assembly. J. Mol. Biol., 2005, 353(1), 68-79.
[60]
Mymrikov, E.V.; Seit-Nebi, A.S.; Gusev, N.B. Large potentials of small heat shock proteins. Physiol. Rev., 2011, 91(4), 1123-1159.
[61]
Assimakopoulou, M.; Sotiropoulou-Bonikou, G.; Maraziotis, T.; Varakis, I. Prognostic significance of Hsp-27 in astrocytic brain tumors: an immunohistochemical study. Physiol. Rev., 1997, 17(4A), 2677-2682.
[62]
Ciocca, D.R.; Calderwood, S.K. Heat shock proteins in cancer: diagnostic, prognostic, predictive, and treatment implications. Cell Stress Chaperones, 2005, 10(2), 86-103.
[63]
Fuqua, S.A.; Oesterreich, S.; Hilsenbeck, S.G.; Von Hoff, D.D.; Eckardt, J.; Osborne, C.K. Heat shock proteins and drug resistance. Breast Cancer Res. Treat., 1994, 32, 67-71.
[64]
Huang, Q.; Ye, J.; Huang, Q.; Chen, W.; Wang, L.; Lin, W.; Lin, J.; Lin, X. Heat shock protein 27 is over-expressed in tumor tissues and increased in sera of patients with gastric adenocarcinoma. Clin. Chem. Lab. Med., 2010, 48(2), 263-269.
[65]
Muzio, L.L.; Leonardi, R.; Mariggio, M.; Mignogna, M.; Rubini, C.; Vinella, A.; Pannone, G.; Giannetti, L.; Serpico, R.; Testa, N. HSP 27 as possible prognostic factor in patients with oral squamous cell carcinoma. Histol. Histopathol., 2004, 19(1), 119-128.
[66]
Kato, K.; Hasegawa, K.; Goto, S.; Inaguma, Y. Dissociation as a result of phosphorylation of an aggregated form of the small stress protein, hsp27. J. Biol. Chem., 1994, 269(15), 11274-11278.
[67]
Hayes, D.; Napoli, V.; Mazurkie, A.; Stafford, W.F.; Graceffa, P. Phosphorylation dependence of hsp27 multimeric size and molecular chaperone function. J. Biol. Chem., 2009, 284(28), 18801-18807.
[68]
Chauhan, D.; Li, G.; Hideshima, T.; Podar, K.; Mitsiades, C.; Mitsiades, N.; Catley, L.; Tai, Y.T.; Hayashi, T.; Shringarpure, R. Hsp27 inhibits release of mitochondrial protein Smac in multiple myeloma cells and confers dexamethasone resistance. Blood, 2003, 102(9), 3379-3386.
[69]
Chen, Y.J.; Lin, Y.P.; Chow, L.P.; Lee, T.C. Proteomic identification of Hsp70 as a new Plk1 substrate in arsenic trioxide‐induced mitotically arrested cells. Proteomics, 2011, 11(22), 4331-4345.
[70]
Chen, Y.J. 1; Lai, K.C.; Kuo, H.H.; Chow, L.P.; Yih, L.H.; Lee, T.C. HSP70 colocalizes with PLK1 at the centrosome and disturbs spindle dynamics in cells arrested in mitosis by arsenic trioxide. Arch. Toxicol., 2014, 88(9), 1711-1723.
[71]
de Cárcer, G. Heat shock protein 90 regulates the metaphase-anaphase transition in a polo-like kinase-dependent manner. Cancer Res., 2004, 64(15), 5106-5112.


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 19
ISSUE: 9
Year: 2019
Page: [742 - 755]
Pages: 14
DOI: 10.2174/1568009619666190211113722
Price: $65

Article Metrics

PDF: 22
HTML: 4
EPUB: 1