Newly constructed network models of different WNT signaling cascades applied to breast cancer expression data

PLoS ONE

Volumn 10, Issue 12, 2015, Pages

  Bayerlová, Michaela ^a   Klemm, Florian ^a   Kramer, Frank ^a   Pukrop, Tobias ^a,b   Beißbarth, Tim ^a   Bleckmann, Annalen ^a  

^a UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^b UNIVERSITY HOSPITAL REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

WNT PROTEIN;

ARTICLE; BREAST CANCER CELL LINE; BREAST CARCINOMA; DATA BASE; GENE EXPRESSION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; RNA SEQUENCE; WNT SIGNALING PATHWAY; BIOLOGICAL MODEL; BREAST TUMOR; FEMALE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PATHOLOGY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TUMOR CELL LINE; VALIDATION STUDY;

BREAST NEOPLASMS; CELL LINE, TUMOR; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MODELS, BIOLOGICAL; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; WNT PROTEINS;

EID: 84955622621     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0144014     Document Type: Article

References (66)

1. Kahn M. Can we safely target the WNT pathway? Nat Rev Drug Discov. 2014; 13: 513-532. doi: 10. 1038/nrd4233 PMID: 24981364
2. Veeman MT, Axelrod JD, Moon RT. A Second Canon: Functions and Mechanisms of β-Catenin-Independent Wnt Signaling. Dev Cell. 2003; 5: 367-377. doi: 10.1016/S1534-5807(03)00266-1 PMID: 12967557
3. Moon RT, Kohn AD, Ferrari GVD, Kaykas A. WNT and β-catenin signalling: diseases and therapies. Nat Rev Genet. 2004; 5: 691-701. doi: 10.1038/nrg1427 PMID: 15372092
4. Nishimura D. BioCarta. Biotech Softw Internet Rep Comput Softw J Sci. 2001; 2: 117-120.
5. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011; 39: D691-D697. doi: 10.1093/nar/gkq1018 PMID: 21067998
6. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004; 32: D277-D280. doi: 10.1093/nar/gkh063 PMID: 14681412
7. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, et al. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009; 37: D674-D679. doi: 10.1093/nar/gkn653 PMID: 18832364
8. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010; 28: 935-942. doi: 10.1038/nbt.1666 PMID: 20829833
9. Kramer F, Bayerlová M, Beißbarth T. R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms. Biology. 2014; 3: 85-100. doi: 10.3390/biology3010085 PMID: 24833336
10. Yost C, Torres M, Miller JR, Huang E, Kimelman D, Moon RT. The axis-inducing activity, stability, and subcellular distribution of beta-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3. Genes Dev. 1996; 10: 1443-1454. doi: 10.1101/gad.10.12.1443 PMID: 8666229
11. Miller JR, Hocking AM, Brown JD, Moon RT. Mechanism and function of signal transduction by the Wnt/beta-catenin and Wnt/Ca2+ pathways. Oncogene. 1999; 18: 7860-7872. PMID: 10630639
12. Amerongen R van, Mikels A, Nusse R. Alternative Wnt Signaling Is Initiated by Distinct Receptors. Sci Signal. 2008; 1: re9-re9. doi: 10.1126/scisignal.135re9 PMID: 18765832
13. Gordon MD, Nusse R. Wnt Signaling: Multiple Pathways, Multiple Receptors, and Multiple Transcription Factors. J Biol Chem. 2006; 281: 22429-22433. doi: 10.1074/jbc.R600015200 PMID: 16793760
14. Amerongen R van, Nusse R. Towards an integrated view of Wnt signaling in. Development. 2009; 136: 3205-3214. doi: 10.1242/dev.033910 PMID: 19736321
15. Anastas JN, Moon RT. WNT signalling pathways as therapeutic targets in cancer. Nat Rev Cancer. 2013; 13: 11-26. doi: 10.1038/nrc3419 PMID: 23258168
16. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature. 2000; 406: 747-752. doi: 10.1038/35021093 PMID: 10963602
17. Sørlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci. 2003; 100: 8418-8423. doi: 10.1073/pnas.0932692100 PMID: 12829800
18. Smid M, Wang Y, Zhang Y, Sieuwerts AM, Yu J, Klijn JGM, et al. Subtypes of Breast Cancer Show Preferential Site of Relapse. Cancer Res. 2008; 68: 3108-3114. doi: 10.1158/0008-5472.CAN-07-5644 PMID: 18451135
19. Khramtsov AI, Khramtsova GF, Tretiakova M, Huo D, Olopade OI, Goss KH. Wnt/beta-catenin pathway activation is enriched in basal-like breast cancers and predicts poor outcome. Am J Pathol. 2010; 176: 2911-2920. doi: 10.2353/ajpath.2010.091125 PMID: 20395444
20. Yang L, Wu X, Wang Y, Zhang K, Wu J, Yuan Y-C, et al. FZD7 has a critical role in cell proliferation in triple negative breast cancer. Oncogene. 2011; 30: 4437-4446. doi: 10.1038/onc.2011.145 PMID: 21532620
21. Zhang S, Chen L, Cui B, Chuang H- Y, Yu J, Wang-Rodriguez J, et al. ROR1 Is Expressed in Human Breast Cancer and Associated with Enhanced Tumor-Cell Growth. PLoS ONE. 2012; 7: e31127. doi: 10.1371/journal.pone.0031127 PMID: 22403610
22. Klemm F, Bleckmann A, Siam L, Chuang HN, Rietkötter E, Behme D, et al. β-catenin-independent WNT signaling in basal-like breast cancer and brain metastasis. Carcinogenesis. 2011; 32: 434-442. doi: 10.1093/carcin/bgq269 PMID: 21173432
23. Henry C, Quadir A, Hawkins NJ, Jary E, Llamosas E, Kumar D, et al. Expression of the novel Wnt receptor ROR2 is increased in breast cancer and may regulate both β-catenin dependent and independent Wnt signalling. J Cancer Res Clin Oncol. 2014; 141: 243-254. doi: 10.1007/s00432-014-1824-y PMID: 25209439
24. Beissbarth T. [18] Interpreting Experimental Results Using Gene Ontologies. In: Oliver AK and B, editor. Methods in Enzymology. Academic Press; 2006. pp. 340-352. Available: http://www.sciencedirect.com/science/article/pii/S0076687906110186
25. Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003; 34: 267-273. doi: 10.1038/ng1180 PMID: 12808457
26. Mitra K, Carvunis A-R, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013; 14: 719-732. doi: 10.1038/nrg3552 PMID: 24045689
27. Bader GD, Cary MP, Sander C. Pathguide: a Pathway Resource List. Nucleic Acids Res. 2006; 34: D504-D506. doi: 10.1093/nar/gkj126 PMID: 16381921
28. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur Ö, Anwar N, et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011; 39: D685-D690. doi: 10.1093/nar/gkq1039 PMID: 21071392
29. Kramer F, Bayerlová M, Klemm F, Bleckmann A, Beißbarth T. rBiopaxParser-an R package to parse, modify and visualize BioPAX data. Bioinformatics. 2013; 29: 520-522. doi: 10.1093/bioinformatics/bts710 PMID: 23274212
30. Kramer F. Integration of Pathway Data as Prior Knowledge into Methods for Network Reconstruction. Göttingen, Georg-August Universität, Diss., 2014. 2014.
31. Clauset A, Newman ME, Moore C. Finding community structure in very large networks. Phys Rev E. 2004; 70: 066111.
32. Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006; Complex Systems: 1695.
33. Bina M, editor. Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO)-Springer . Humana Press; 2006. Available: http://link.springer.com/protocol/10.1385/1-59745-097-9:175
34. Cappellen D, Schlange T, Bauer M, Maurer F, Hynes NE. Novel c-MYC target genes mediate differential effects on cell proliferation and migration. EMBO Rep. 2007; 8: 70-76. doi: 10.1038/sj.embor. 7400849 PMID: 17159920
35. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4: 249-264. doi: 10.1093/biostatistics/4.2.249 PMID: 12925520
36. Smyth GK. limma: Linear Models for Microarray Data. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer New York; 2005. pp. 397-420. Available: http://link.springer.com/chapter/10.1007/0-387- 29362-0-23
37. Hommel G. A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika. 1988; 75: 383-386. doi: 10.1093/biomet/75.2.383
38. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNAseq aligner. Bioinformatics. 2013; 29: 15-21. doi: 10.1093/bioinformatics/bts635 PMID: 23104886
39. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12: 323. doi: 10.1186/1471-2105-12-323 PMID: 21816040
40. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26: 139-140. doi: 10.1093/bioinformatics/btp616 PMID: 19910308
41. Takahashi H, Matsuyama A. An approximate solution for the Steiner problem in graphs. Math Jpn. 1980; 24: 573-577.
42. Sadeghi A, Fröhlich H. Steiner tree methods for optimal sub-network identification: an empirical study. BMC Bioinformatics. 2013; 14: 144. doi: 10.1186/1471-2105-14-144 PMID: 23627667
43. Fruchterman TMJ, Reingold EM. Graph drawing by force-directed placement. Softw Pract Exp. 1991; 21: 1129-1164. doi: 10.1002/spe.4380211102
44. Dijksterhuis JP, Petersen J, Schulte G. WNT/Frizzled signalling: receptor-ligand selectivity with focus on FZD-G protein signalling and its physiological relevance: IUPHAR Review 3. Br J Pharmacol. 2014; 171: 1195-1209. doi: 10.1111/bph.12364 PMID: 24032637
45. Chen J, Xie Z-R, Wu Y. Computational Modeling of the Interplay between Cadherin-Mediated Cell Adhesion and Wnt Signaling Pathway. PLoS ONE. 2014; 9: e100702. doi: 10.1371/journal.pone. 0100702 PMID: 24967587
46. van Leeuwen IMM, Byrne HM, Jensen OE, King JR. Elucidating the interactions between the adhesive and transcriptional functions of -catenin in normal and cancerous cells. J Theor Biol. 2007; 247: 77-102. doi: 10.1016/j.jtbi.2007.01.019 PMID: 17382967
47. Katoh M, Katoh M. WNT Signaling Pathway and Stem Cell Signaling Network. Clin Cancer Res. 2007; 13: 4042-4045. doi: 10.1158/1078-0432.CCR-06-2316 PMID: 17634527
48. Holland JD, Klaus A, Garratt AN, Birchmeier W. Wnt signaling in stem and cancer stem cells. Curr Opin Cell Biol. 2013; 25: 254-264. doi: 10.1016/j.ceb.2013.01.004 PMID: 23347562
49. Grumolato L, Liu G, Mong P, Mudbhary R, Biswas R, Arroyave R, et al. Canonical and noncanonical Wnts use a common mechanism to activate completely unrelated coreceptors. Genes Dev. 2010; 24: 2517-2530. doi: 10.1101/gad.1957710 PMID: 21078818
50. Gao C, Chen Y-G. Dishevelled: The hub of Wnt signaling. Cell Signal. 2010; 22: 717-727. doi: 10. 1016/j.cellsig.2009.11.021 PMID: 20006983
51. Kühl M, Sheldahl LC, Malbon CC, Moon RT. Ca2+/Calmodulin-dependent Protein Kinase II Is Stimulated by Wnt and Frizzled Homologs and Promotes Ventral Cell Fates in Xenopus. J Biol Chem. 2000; 275: 12701-12711. doi: 10.1074/jbc.275.17.12701 PMID: 10777564
52. Critchley DR, Gingras AR. Talin at a glance. J Cell Sci. 2008; 121: 1345-1347. doi: 10.1242/jcs.018085 PMID: 18434644
53. He J, Sheng T, Stelter AA, Li C, Zhang X, Sinha M, et al. Suppressing Wnt Signaling by the Hedgehog Pathway through sFRP-1. J Biol Chem. 2006; 281: 35598-35602. doi: 10.1074/jbc.C600200200 PMID: 17035233
54. Cowling VH, D'Cruz CM, Chodosh LA, Cole MD. c-Myc Transforms Human Mammary Epithelial Cells through Repression of the Wnt Inhibitors DKK1 and SFRP1. Mol Cell Biol. 2007; 27: 5135-5146. doi: 10.1128/MCB.02282-06 PMID: 17485441
55. Chuang H-Y, Lee E, Liu Y-T, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007; 3. doi: 10.1038/msb4100180
56. De A. Wnt/Ca2+ signaling pathway: a brief overview. Acta Biochim Biophys Sin. 2011; 43: 745-756. doi: 10.1093/abbs/gmr079 PMID: 21903638
57. Choi H-K, Choi K-C, Yoo J-Y, Song M, Ko SJ, Kim CH, et al. Reversible SUMOylation of TBL1-TBLR1 Regulates β-Catenin-Mediated Wnt Signaling. Mol Cell. 2011; 43: 203-216. doi: 10.1016/j.molcel. 2011.05.027 PMID: 21777810
58. Fröhlich H, Fellmann M, Sültmann H, Poustka A, Beissbarth T. Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. Bioinformatics. 2008; 24: 2650-2656. doi: 10.1093/bioinformatics/btm634 PMID: 18227117
59. Bender C, Henjes F, Fröhlich H, Wiemann S, Korf U, Beißbarth T. Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data. Bioinformatics. 2010; 26: i596-i602. doi: 10.1093/bioinformatics/btq385 PMID: 20823327
60. Zhao S, Fung-Leung W-P, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells. PLoS ONE. 2014; 9. doi: 10.1371/journal.pone.0078644
61. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y. Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data. PLoS ONE. 2013; 8: e71462. doi: 10.1371/journal. pone.0071462 PMID: 23977046
62. Müller MR, Rao A. NFAT, immunity and cancer: a transcription factor comes of age. Nat Rev Immunol. 2010; 10: 645-656. doi: 10.1038/nri2818 PMID: 20725108
63. Chen EI, Hewel J, Krueger JS, Tiraby C, Weber MR, Kralli A, et al. Adaptation of Energy Metabolism in Breast Cancer Brain Metastases. Cancer Res. 2007; 67: 1472-1486. doi: 10.1158/0008-5472.CAN- 06-3137 PMID: 17308085
64. Bhalla K, Hwang BJ, Dewi RE, Ou L, TwaddelW, Fang H, et al. PGC1α Promotes Tumor Growth by Inducing Gene Expression Programs Supporting Lipogenesis. Cancer Res. 2011; 71: 6888-6898. doi: 10.1158/0008-5472.CAN-11-1011 PMID: 21914785
65. Luga V, Zhang L, Viloria-Petit AM, Ogunjimi AA, Inanlou MR, Chiu E, et al. Exosomes Mediate Stromal Mobilization of Autocrine Wnt-PCP Signaling in Breast Cancer Cell Migration. Cell. 2012; 151: 1542-1556. doi: 10.1016/j.cell.2012.11.024 PMID: 23260141
66. Yu K- D, Zhu R, Zhan M, Rodriguez AA, Yang W, Wong S, et al. Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple-Negative Breast Cancer. Clin Cancer Res. 2013; 19: 2723-2733. doi: 10.1158/1078-0432.CCR-12-2986 PMID: 23549873