2,740
Views
20
CrossRef citations to date
0
Altmetric
Report

Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures

, , &
Pages 2262-2280 | Received 03 Apr 2014, Accepted 17 May 2014, Published online: 30 May 2014

References

  • Siegel R, Naishadham D, Jemal A. Cancer statistics, 2012. CA Cancer J Clin 2012; 62:10 - 29; http://dx.doi.org/10.3322/caac.20138; PMID: 22237781
  • Cho KR, Shih IeM. Ovarian cancer. Annu Rev Pathol 2009; 4:287 - 313; http://dx.doi.org/10.1146/annurev.pathol.4.110807.092246; PMID: 18842102
  • Tuma RS. Origin of ovarian cancer may have implications for screening. J Natl Cancer Inst 2010; 102:11 - 3; http://dx.doi.org/10.1093/jnci/djp495; PMID: 20023201
  • Mankoo PK, Shen R, Schultz N, Levine DA, Sander C. Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. PLoS One 2011; 6:e24709; http://dx.doi.org/10.1371/journal.pone.0024709; PMID: 22073136
  • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474:609 - 15; http://dx.doi.org/10.1038/nature10166; PMID: 21720365
  • Tang Z, Ow GS, Thiery JP, Ivshina AV, Kuznetsov VA. Meta-analysis of transcriptome reveals let-7b as an unfavorable prognostic biomarker and predicts molecular and clinical subclasses in high-grade serous ovarian carcinoma. Int J Cancer 2014; 134:306 - 18; PMID: 23825028
  • Matias-Guiu X, Davidson B. Prognostic biomarkers in endometrial and ovarian carcinoma. Virchows Arch 2014; 464:315 - 31; http://dx.doi.org/10.1007/s00428-013-1509-y; PMID: 24504546
  • Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014; 505:495 - 501; http://dx.doi.org/10.1038/nature12912; PMID: 24390350
  • Walsh T, Casadei S, Lee MK, Pennil CC, Nord AS, Thornton AM, Roeb W, Agnew KJ, Stray SM, Wickramanayake A, et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A 2011; 108:18032 - 7; http://dx.doi.org/10.1073/pnas.1115052108; PMID: 22006311
  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646 - 74; http://dx.doi.org/10.1016/j.cell.2011.02.013; PMID: 21376230
  • McGowan CH. Checking in on Cds1 (Chk2): A checkpoint kinase and tumor suppressor. Bioessays 2002; 24:502 - 11; http://dx.doi.org/10.1002/bies.10101; PMID: 12111733
  • Baysal BE, DeLoia JA, Willett-Brozick JE, Goodman MT, Brady MF, Modugno F, Lynch HT, Conley YP, Watson P, Gallion HH. Analysis of CHEK2 gene for ovarian cancer susceptibility. Gynecol Oncol 2004; 95:62 - 9; http://dx.doi.org/10.1016/j.ygyno.2004.07.015; PMID: 15385111
  • Szymanska-Pasternak J, Szymanska A, Medrek K, Imyanitov EN, Cybulski C, Gorski B, Magnowski P, Dziuba I, Gugala K, Debniak B, et al. CHEK2 variants predispose to benign, borderline and low-grade invasive ovarian tumors. Gynecol Oncol 2006; 102:429 - 31; http://dx.doi.org/10.1016/j.ygyno.2006.05.040; PMID: 16828850
  • Krylova NY, Ponomariova DN, Sherina NY, Ogorodnikova NY, Logvinov DA, Porhanova NV, Lobeiko OS, Urmancheyeva AF, Maximov SY, Togo AV, et al. CHEK2 1100 delC mutation in Russian ovarian cancer patients. Hered Cancer Clin Pract 2007; 5:153 - 6; http://dx.doi.org/10.1186/1897-4287-5-3-153; PMID: 19725991
  • Słojewski M, Złowocka E, Cybulski C, Górski B, Debniak T, Wokołorczyk D, Matyjasik J, Sikorski A, Lubiński J. CHEK2 germline mutations correlate with recurrence rate in patients with superficial bladder cancer. Ann Acad Med Stetin 2008; 54:115 - 21; PMID: 19839522
  • Angelova SG, Krasteva ME, Gospodinova ZI, Georgieva EI. CHEK2 gene alterations independently increase the risk of death from breast cancer in Bulgarian patients. Neoplasma 2012; 59:622 - 30; http://dx.doi.org/10.4149/neo_2012_079; PMID: 22862163
  • Schmidt MK, Tollenaar RA, de Kemp SR, Broeks A, Cornelisse CJ, Smit VT, Peterse JL, van Leeuwen FE, Van’t Veer LJ. Breast cancer survival and tumor characteristics in premenopausal women carrying the CHEK2*1100delC germline mutation. J Clin Oncol 2007; 25:64 - 9; http://dx.doi.org/10.1200/JCO.2006.06.3024; PMID: 17132695
  • de Bock GH, Schutte M, Krol-Warmerdam EM, Seynaeve C, Blom J, Brekelmans CT, Meijers-Heijboer H, van Asperen CJ, Cornelisse CJ, Devilee P, et al. Tumour characteristics and prognosis of breast cancer patients carrying the germline CHEK2*1100delC variant. J Med Genet 2004; 41:731 - 5; http://dx.doi.org/10.1136/jmg.2004.019737; PMID: 15466005
  • Simon M, Ludwig M, Fimmers R, Mahlberg R, Müller-Erkwoh A, Köster G, Schramm J. Variant of the CHEK2 gene as a prognostic marker in glioblastoma multiforme. Neurosurgery 2006; 59:1078 - 85, discussion 1085; PMID: 17016233
  • Barillot E, Calzone L, Hupé P, Vert J, Zinovyev A. Computation Systems Biology of Cancer. London: CRC Press, 2012.
  • Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. Mol Biosyst 2010; 6:1767 - 72; http://dx.doi.org/10.1039/c004796c; PMID: 20617253
  • Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 2003; 12:205 - 16; http://dx.doi.org/10.1093/hmg/ddg055; PMID: 12554675
  • Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM. A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 2007; 315:525 - 8; http://dx.doi.org/10.1126/science.1135308; PMID: 17185560
  • Kuznetsov VA. Family of skewed distributions associated with the gene expression and proteome evolution. Signal Process 2003; 83:889 - 910; http://dx.doi.org/10.1016/S0165-1684(02)00481-4
  • Kuznetsov VA. Hypergeometric Model of Evolution of Conserved Protein Coding Sequences in the Proteomes. Fluctuation and Noise Letters 2003; 3:L295 - 324; http://dx.doi.org/10.1142/S0219477503001397
  • Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ, Stratton MR. Deciphering signatures of mutational processes operative in human cancer. Cell Rep 2013; 3:246 - 59; http://dx.doi.org/10.1016/j.celrep.2012.12.008; PMID: 23318258
  • Lynch HT, Lynch PM, Lanspa SJ, Snyder CL, Lynch JF, Boland CR. Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications. Clin Genet 2009; 76:1 - 18; http://dx.doi.org/10.1111/j.1399-0004.2009.01230.x; PMID: 19659756
  • Bashashati A, Ha G, Tone A, Ding J, Prentice LM, Roth A, Rosner J, Shumansky K, Kalloger S, Senz J, et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol 2013; 231:21 - 34; http://dx.doi.org/10.1002/path.4230; PMID: 23780408
  • Bolton KL, Chenevix-Trench G, Goh C, Sadetzki S, Ramus SJ, Karlan BY, Lambrechts D, Despierre E, Barrowdale D, McGuffog L, et al, EMBRACE, kConFab Investigators, Cancer Genome Atlas Research Network. Association between BRCA1 and BRCA2 mutations and survival in women with invasive epithelial ovarian cancer. JAMA 2012; 307:382 - 90; http://dx.doi.org/10.1001/jama.2012.20; PMID: 22274685
  • McLaughlin JR, Rosen B, Moody J, Pal T, Fan I, Shaw PA, Risch HA, Sellers TA, Sun P, Narod SA. Long-term ovarian cancer survival associated with mutation in BRCA1 or BRCA2. J Natl Cancer Inst 2013; 105:141 - 8; http://dx.doi.org/10.1093/jnci/djs494; PMID: 23257159
  • Chrisanthar R, Knappskog S, Løkkevik E, Anker G, Østenstad B, Lundgren S, Berge EO, Risberg T, Mjaaland I, Maehle L, et al. CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer. PLoS One 2008; 3:e3062; http://dx.doi.org/10.1371/journal.pone.0003062; PMID: 18725978
  • Motakis E, Ivshina AV, Kuznetsov VA. Data-driven approach to predict survival of cancer patients: estimation of microarray genes’ prediction significance by Cox proportional hazard regression model. IEEE Eng Med Biol Mag 2009; 28:58 - 66; http://dx.doi.org/10.1109/MEMB.2009.932937; PMID: 19622426
  • Magrane M, Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011; 2011:bar009; http://dx.doi.org/10.1093/database/bar009; PMID: 21447597
  • Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res 2011; 39:D261 - 7; http://dx.doi.org/10.1093/nar/gkq1104; PMID: 21062810
  • Yoda A, Xu XZ, Onishi N, Toyoshima K, Fujimoto H, Kato N, Oishi I, Kondo T, Minami Y. Intrinsic kinase activity and SQ/TQ domain of Chk2 kinase as well as N-terminal domain of Wip1 phosphatase are required for regulation of Chk2 by Wip1. J Biol Chem 2006; 281:24847 - 62; http://dx.doi.org/10.1074/jbc.M600403200; PMID: 16798742
  • Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999; 294:1351 - 62; http://dx.doi.org/10.1006/jmbi.1999.3310; PMID: 10600390
  • Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 2007; 8:R250; http://dx.doi.org/10.1186/gb-2007-8-11-r250; PMID: 18039369
  • Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM, Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 2013; 45:1113 - 20; http://dx.doi.org/10.1038/ng.2764; PMID: 24071849
  • Cai Z, Chehab NH, Pavletich NP. Structure and activation mechanism of the CHK2 DNA damage checkpoint kinase. Mol Cell 2009; 35:818 - 29; http://dx.doi.org/10.1016/j.molcel.2009.09.007; PMID: 19782031
  • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234:779 - 815; http://dx.doi.org/10.1006/jmbi.1993.1626; PMID: 8254673
  • Zannini L, Lecis D, Lisanti S, Benetti R, Buscemi G, Schneider C, Delia D. Karyopherin-alpha2 protein interacts with Chk2 and contributes to its nuclear import. J Biol Chem 2003; 278:42346 - 51; http://dx.doi.org/10.1074/jbc.M303304200; PMID: 12909615
  • Nakai K, Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999; 24:34 - 6; http://dx.doi.org/10.1016/S0968-0004(98)01336-X; PMID: 10087920
  • Kosugi S, Hasebe M, Tomita M, Yanagawa H. Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A 2009; 106:10171 - 6; http://dx.doi.org/10.1073/pnas.0900604106; PMID: 19520826
  • Zhang P, Gao W, Li H, Reed E, Chen F. Inducible degradation of checkpoint kinase 2 links to cisplatin-induced resistance in ovarian cancer cells. Biochem Biophys Res Commun 2005; 328:567 - 72; http://dx.doi.org/10.1016/j.bbrc.2005.01.007; PMID: 15694385
  • He Z, Yang C, Guo G, Li N, Yu W. Motif-All: discovering all phosphorylation motifs. BMC Bioinformatics 2011; 12:Suppl 1 S22; http://dx.doi.org/10.1186/1471-2105-12-S1-S22; PMID: 21342552
  • Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform 2011; 4:22 - 35; http://dx.doi.org/10.4172/jpb.1000163; PMID: 21720494
  • Lahiry P, Torkamani A, Schork NJ, Hegele RA. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet 2010; 11:60 - 74; http://dx.doi.org/10.1038/nrg2707; PMID: 20019687
  • Tsatsanis C, Spandidos DA. The role of oncogenic kinases in human cancer (Review). [Review] Int J Mol Med 2000; 5:583 - 90; PMID: 10812005
  • Dancey J, Sausville EA. Issues and progress with protein kinase inhibitors for cancer treatment. Nat Rev Drug Discov 2003; 2:296 - 313; http://dx.doi.org/10.1038/nrd1066; PMID: 12669029
  • Pearson MA, Fabbro D. Targeting protein kinases in cancer therapy: a success?. Expert Rev Anticancer Ther 2004; 4:1113 - 24; http://dx.doi.org/10.1586/14737140.4.6.1113; PMID: 15606337
  • Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods 2013; 10:1108 - 15; http://dx.doi.org/10.1038/nmeth.2651; PMID: 24037242
  • Williams LH, Choong D, Johnson SA, Campbell IG. Genetic and epigenetic analysis of CHEK2 in sporadic breast, colon, and ovarian cancers. Clin Cancer Res 2006; 12:6967 - 72; http://dx.doi.org/10.1158/1078-0432.CCR-06-1770; PMID: 17145815
  • Jobson AG, Lountos GT, Lorenzi PL, Llamas J, Connelly J, Cerna D, Tropea JE, Onda A, Zoppoli G, Kondapaka S, et al. Cellular inhibition of checkpoint kinase 2 (Chk2) and potentiation of camptothecins and radiation by the novel Chk2 inhibitor PV1019 [7-nitro-1H-indole-2-carboxylic acid 4-[1-(guanidinohydrazone)-ethyl]-phenyl-amide]. J Pharmacol Exp Ther 2009; 331:816 - 26; http://dx.doi.org/10.1124/jpet.109.154997; PMID: 19741151
  • Yu Q, Rose JH, Zhang H, Pommier Y. Antisense inhibition of Chk2/hCds1 expression attenuates DNA damage-induced S and G2 checkpoints and enhances apoptotic activity in HEK-293 cells. FEBS Lett 2001; 505:7 - 12; http://dx.doi.org/10.1016/S0014-5793(01)02756-9; PMID: 11557032
  • Vakifahmetoglu H, Olsson M, Tamm C, Heidari N, Orrenius S, Zhivotovsky B. DNA damage induces two distinct modes of cell death in ovarian carcinomas. Cell Death Differ 2008; 15:555 - 66; http://dx.doi.org/10.1038/sj.cdd.4402286; PMID: 18064041
  • Ghosh JC, Dohi T, Raskett CM, Kowalik TF, Altieri DC. Activated checkpoint kinase 2 provides a survival signal for tumor cells. Cancer Res 2006; 66:11576 - 9; http://dx.doi.org/10.1158/0008-5472.CAN-06-3095; PMID: 17178848
  • Alkema NG, Tomar T, van der Zee AG, Everts M, Meersma GJ, Hollema H, de Jong S, van Vugt MA, Wisman GB. Checkpoint kinase 2 (Chk2) supports sensitivity to platinum-based treatment in high grade serous ovarian cancer. Gynecol Oncol 2014; http://dx.doi.org/10.1016/j.ygyno.2014.03.557; PMID: 24657486
  • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8:118 - 27; http://dx.doi.org/10.1093/biostatistics/kxj037; PMID: 16632515
  • Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, et al, International Cancer Genome Consortium. International network of cancer genome projects. Nature 2010; 464:993 - 8; http://dx.doi.org/10.1038/nature08987; PMID: 20393554
  • Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics 2012; Chapter 1:Unit1 4.
  • de Hoon MJ, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004; 20:1453 - 4; http://dx.doi.org/10.1093/bioinformatics/bth078; PMID: 14871861
  • Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998; 95:14863 - 8; http://dx.doi.org/10.1073/pnas.95.25.14863; PMID: 9843981
  • Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44 - 57; http://dx.doi.org/10.1038/nprot.2008.211; PMID: 19131956
  • Rich JT, Neely JG, Paniello RC, Voelker CC, Nussenbaum B, Wang EW. A practical guide to understanding Kaplan–Meier curves. Otolaryngol Head Neck Surg 2010; 143:331 - 6; http://dx.doi.org/10.1016/j.otohns.2010.05.007; PMID: 20723767
  • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007; 35:W522-5; http://dx.doi.org/10.1093/nar/gkm276; PMID: 17488841
  • Case DA, Darden TA. T.E. Cheatham I, Simmerling CL, Wang J, Duke RE, et al. AMBER 12. University of California, San Francisco., 2012.
  • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006; 65:712 - 25; http://dx.doi.org/10.1002/prot.21123; PMID: 16981200
  • Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput 2012; 8:1542 - 55; http://dx.doi.org/10.1021/ct200909j; PMID: 22582031
  • Pereira M, Verma CS, Fuentes G. Differences in the binding affinities of ErbB family: heterogeneity in the prediction of resistance mutants. PLoS One 2013; 8:e77054; http://dx.doi.org/10.1371/journal.pone.0077054; PMID: 24194858
  • Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1.3r1. 2010