Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks

Molecular BioSystems

Volumn 10, Issue 1, 2014, Pages 45-53

  Song, J ^a   Wang, Z ^a   Ewing, R M ^b  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; PROTEOME; WNT3A PROTEIN; WNT3A PROTEIN, HUMAN;

ARTICLE; COLORECTAL TUMOR; GENE EXPRESSION REGULATION; GENETICS; HCT116 CELL LINE; HEK293 CELL LINE; HUMAN; METABOLISM; PATHOLOGY; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; WNT SIGNALING PATHWAY;

BETA CATENIN; COLORECTAL NEOPLASMS; GENE EXPRESSION REGULATION, NEOPLASTIC; HCT116 CELLS; HEK293 CELLS; HUMANS; PROTEIN INTERACTION MAPS; PROTEOME; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; WNT SIGNALING PATHWAY; WNT3A PROTEIN;

EID: 84889021354     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c3mb70417c     Document Type: Article

References (43)

1. C. Y. Logan R. Nusse The Wnt signaling pathway in development and disease Annu. Rev. Cell Dev. Biol. 2004 20 781 810
2. H. Clevers Wnt/beta-catenin signaling in development and disease Cell 2006 127 3 469 480 10.1016/j.cell.2006.10.018
3. S. Angers R. T. Moon Proximal events in Wnt signal transduction Nat. Rev. Mol. Cell Biol. 2009 10 7 468 477 10.1038/nrm2717
4. P. J. Morin A. B. Sparks V. Korinek N. Barker H. Clevers B. Vogelstein et al., Activation of beta-catenin-Tcf signaling in colon cancer by mutations in beta-catenin or APC Science 1997 275 5307 1787 1790
5. K. W. Kinzler B. Vogelstein Lessons from hereditary colorectal cancer Cell 1996 87 2 159 170
6. W. J. Nelson R. Nusse Convergence of Wnt, beta-catenin, and cadherin pathways Science 2004 303 5663 1483 1487 10.1126/science.1094291
7. T. Valenta G. Hausmann K. Basler The many faces and functions of β-catenin EMBO J. 2012 31 12 2714 2736 10.1038/emboj.2012.150
8. R. Dasgupta Functional genomic approaches targeting the wnt signaling network Curr. Drug Targets 2009 10 7 620 631
9. J. D. Berndt T. L. Biechele R. T. Moon M. B. Major Integrative analysis of genome-wide RNA interference screens Sci. Signaling 2009 2 70 pt4 10.1126/scisignal.270pt4
10. W. Tang M. Dodge D. Gundapaneni C. Michnoff M. Roth L. Lum A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer Proc. Natl. Acad. Sci. U. S. A. 2008 105 28 9697 9702
11. T. S. Gujral G. MacBeath A system-wide investigation of the dynamics of Wnt signaling reveals novel phases of transcriptional regulation PLoS One 2010 5 4 e10024 10.1371/journal.pone.0010024
12. S. Vijayakumar G. Liu I. A. Rus S. Yao Y. Chen G. Akiri et al., High-frequency canonical Wnt activation in multiple sarcoma subtypes drives proliferation through a TCF/β-catenin target gene, CDC25A Cancer Cell 2011 19 5 601 612
13. L.-Y. Tang N. Deng L.-S. Wang J. Dai Z.-L. Wang X.-S. Jiang et al., Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction Mol. Cell. Proteomics 2007 6 11 1952 1967
14. M. B. Major N. D. Camp J. D. Berndt X. Yi S. J. Goldenberg C. Hubbert et al., Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling Science 2007 316 5827 1043 1046 10.1126/science/1141515
15. S. Angers C. J. Thorpe T. L. Biechele S. J. Goldenberg N. Zheng M. J. MacCoss et al., The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation Nat. Cell Biol. 2006 8 4 348 357 10.1038/ncb1381
16. R. Pancratov R. Dasgupta Postgenomic technologies targeting the Wnt signaling network Wiley Interdiscip. Rev.: Syst. Biol. Med. 2011 3 6 649 665 10.1002/wsbm.140
17. V. Hatini P. Bokor R. Goto-Mandeville S. DiNardo Tissue- and stage-specific modulation of Wingless signaling by the segment polarity gene lines Genes Dev. 2000 14 11 1364 1376
18. G. Roël F. S. Hamilton Y. Gent A. A. Bain O. Destrée S. Hoppler Lef-1 and Tcf-3 transcription factors mediate tissue-specific Wnt signaling during Xenopus development Curr. Biol. 2002 12 22 1941 1945
19. M. Gassmann B. Grenacher B. Rohde J. Vogel Quantifying Western blots: pitfalls of densitometry Electrophoresis 2009 30 11 1845 1855
20. H. Y. Tan T. W. Ng Accurate step wedge calibration for densitometry of electrophoresis gels Opt. Commun. 2008 281 10 3013 3017 10.1016/j.optcom.2008. 01.012
21. C. R. Jiménez L. Huang Y. Qiu A. L. Burlingame In-gel digestion of proteins for MALDI-MS fingerprint mapping Curr. Protoc. Protein Sci. 2001
22. B. C. Searle Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies Proteomics 2010 10 6 1265 1269
23. A. I. Nesvizhskii A. Keller E. Kolker R. Aebersold A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003 75 17 4646 4658
24. B. L. Zybailov L. Florens M. P. Washburn Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors Mol. BioSyst. 2007 3 5 354 360 10.1039/b701483j
25. R. M. Ewing P. Chu H. Li P. Taylor S. Climie L. McBroom et al., Large-scale mapping of human protein-protein interactions by mass spectrometry Mol. Syst. Biol. 2007 3 89
26. D. Mellacheruvu Z. Wright A. L. Couzens J.-P. Lambert N. A. St-Denis T. Li et al., The CRAPome: a contaminant repository for affinity purification-mass spectrometry data Nat. Methods 2013 10 8 730 736
27. T. A. Chan Z. Wang L. H. Dang B. Vogelstein K. W. Kinzler Targeted inactivation of CTNNB1 reveals unexpected effects of beta-catenin mutation Proc. Natl. Acad. Sci. U. S. A. 2002 99 12 8265 8270 10.1073/pnas.082240999
28. M. Ilyas beta-Catenin mutations in cell lines established from human colorectal cancers Proc. Natl. Acad. Sci. U. S. A. 1997 94 19 10330 10334
29. L.-Y. Tang N. Deng L.-S. Wang J. Dai Z.-L. Wang X.-S. Jiang et al., Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction Mol. Cell. Proteomics 2007 6 11 1952 1967
30. E. Rampazzo L. Persano F. Pistollato E. Moro C. Frasson P. Porazzi et al., Wnt activation promotes neuronal differentiation of Glioblastoma Cell Death Dis. 2013 4 e500 10.1038/cddis.2013.32
31. Z. Klapholz-Brown G. G. Walmsley Y. M. Nusse R. Nusse P. O. Brown Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments PLoS One 2007 2 9 e945 10.1371/journal.pone.0000945
32. F. Leve J. A. Morgado-Díaz Rho GTPase signaling in the development of colorectal cancer J. Cell. Biochem. 2012 113 8 2549 2559
33. J. Song Y. Hao Z. Du Z. Wang R. M. Ewing Identifying Novel Protein Complexes in Cancer Cells Using Epitope-Tagging of Endogenous Human Genes and Affinity-Purification Mass Spectrometry J. Proteome Res. 2012 10.1021/pr300598t
34. O. Maeda N. Usami M. Kondo M. Takahashi H. Goto K. Shimokata et al., Plakoglobin (gamma-catenin) has TCF/LEF family-dependent transcriptional activity in beta-catenin-deficient cell line Oncogene 2004 23 4 964 972
35. C.-H. Chen S.-M. Chuang M.-F. Yang J.-W. Liao S.-L. Yu J. J. W. Chen A novel function of YWHAZ/β-catenin axis in promoting epithelial-mesenchymal transition and lung cancer metastasis Mol. Cancer Res. 2012 10 10 1319 1331
36. Q. Tian M. C. Feetham W. A. Tao X. C. He L. Li R. Aebersold et al., Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt Proc. Natl. Acad. Sci. U. S. A. 2004 101 43 15370 15375 10.1073/pnas.0406499101
37. J. Liu A. G. Bang C. Kintner A. P. Orth S. K. Chanda S. Ding et al., Identification of the Wnt signaling activator leucine-rich repeat in Flightless interaction protein 2 by a genome-wide functional analysis Proc. Natl. Acad. Sci. U. S. A. 2005 102 6 1927 1932
38. B. Carpenter K. J. Hill M. Charalambous K. J. Wagner D. Lahiri D. I. James et al., BASP1 is a transcriptional cosuppressor for the Wilms' tumor suppressor protein WT1 Mol. Cell. Biol. 2004 24 2 537 549
39. S. J. Goodfellow M. R. Rebello E. Toska L. A. H. Zeef S. G. Rudd K. F. Medler et al., WT1 and its transcriptional cofactor BASP1 redirect the differentiation pathway of an established blood cell line Biochem. J. 2011 435 1 113 125
40. M. B. Major N. D. Camp J. D. Berndt X. Yi S. J. Goldenberg C. Hubbert et al., Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling Science 2007 316 5827 1043 1046
41. M. N. Rivera W. J. Kim J. Wells A. Stone A. Burger E. J. Coffman et al., The tumor suppressor WTX shuttles to the nucleus and modulates WT1 activity Proc. Natl. Acad. Sci. U. S. A. 2009 106 20 8338 8343 10.1073/pnas.0811349106
42. M. Beck A. Schmidt J. Malmstroem M. Claassen A. Ori A. Szymborska et al., The quantitative proteome of a human cell line Mol. Syst. Biol. 2011 7 1 549
43. M. B. Major B. S. Roberts J. D. Berndt S. Marine J. Anastas N. Chung et al., New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening Sci. Signaling 2008 1 45 ra12