Protein interactome of muscle invasive bladder cancer

PLoS ONE

Volumn 10, Issue 1, 2015, Pages

  Bhat, Akshay ^a,b   Heinzel, Andreas ^c   Mayer, Bernd ^c   Perco, Paul ^c   Mühlberger, Irmgard ^c   Husi, Holger ^d   Merseburger, Axel S ^e   Zoidakis, Jerome ^f   Vlahou, Antonia ^f   Schanstra, Joost P ^g,h   Mischak, Harald ^b,d   Jankowski, Vera ⁱ  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b MOSAIQUES DIAGNOSTICS GMBH   (Germany)

^c Emergentec Biodevelopment GmbH   (Austria)

^d UNIVERSITY OF GLASGOW   (United Kingdom)

^e HANNOVER MEDICAL SCHOOL   (Germany)

^f Academy of Athens Biomedical Research Foundation   (Greece)

^g INSERM   (France)

^h UNIVERSITÉ PAUL SABATIER   (France)

ⁱ Institute for Molecular Cardiovascular Research IMCAR   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

NEUROTROPHIN; NERVE GROWTH FACTOR; TUMOR MARKER;

ACTIN FILAMENT; ARTICLE; CANCER GROWTH; ENDOCYTOSIS; GENE EXPRESSION PROFILING; GENETIC CODE; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR MECHANICS; MOLECULAR MODEL; MUSCLE INVASIVE BLADDER CANCER; PHENOTYPE; PROTEIN ANALYSIS; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMATIC REVIEW; BLADDER TUMOR; FACTUAL DATABASE; METABOLISM; MUSCLE TUMOR; PATHOLOGY; PROTEIN PROTEIN INTERACTION; SECONDARY;

ACTIN CYTOSKELETON; BIOMARKERS, TUMOR; DATABASES, FACTUAL; ENDOCYTOSIS; HUMANS; MUSCLE NEOPLASMS; NERVE GROWTH FACTORS; PHENOTYPE; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION; URINARY BLADDER NEOPLASMS;

EID: 84920771366     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116404     Document Type: Article

References (65)

1. Siegel R, Naishadham D, Jemal A (2013) Cancer statistics, 2013. CA Cancer J Clin 63: 11-30. doi: 10.3322/caac.21166 PMID: 23335087
2. Vishnu P, Mathew J, Tan WW (2011) Current therapeutic strategies for invasive and metastatic bladder cancer. Onco Targets Ther 4: 97-113. doi: 10.2147/OTT.S22875 PMID: 21792316
3. Mitra AP, Cote RJ (2009) Molecular pathogenesis and diagnostics of bladder cancer. Annu Rev Pathol 4: 251-285. doi: 10.1146/annurev.pathol.4.110807.092230 PMID: 18840072
4. Henning A, Wehrberger M, Madersbacher S, Pycha A, Martini T, et al. (2013) Do differences in clinical symptoms and referral patterns contribute to the gender gap in bladder cancer? BJU Int 112: 68-73. doi: 10.1111/j.1464-410X.2012.11661.x PMID: 23320798
5. Raman JD, Shariat SF, Karakiewicz PI, Lotan Y, Sagalowsky AI, et al. (2011) Does preoperative symptom classification impact prognosis in patients with clinically localized upper-tract urothelial carcinoma managed by radical nephroureterectomy? Urol Oncol 29: 716-723. doi: 10.1016/j.urolonc.2009.11.007 PMID: 20056458
6. Di Pierro GB, Gulia C, Cristini C, Fraietta G, Marini L, et al. (2012) Bladder cancer: a simple model becomes complex. Curr Genomics 13: 395-415. doi: 10.2174/138920212801619232 PMID: 23372425
7. Xiao J, Yiqing Q (2013) Bioinformatics analysis of the gene expression profile in Bladder carcinoma. Genet Mol Biol 36: 287-291. doi: 10.1590/S1415-47572013005000015 PMID: 23885213
8. Cauberg Evelyne CC, de la Rosette JJMCH, de Reijke TM (2011) Emerging optical techniques in advanced cystoscopy for bladder cancer diagnosis: A review of the current literature. Indian J Urol 27: 245-251. doi: 10.4103/0970-1591.82845 PMID: 21814317
9. Emmert-Streib F, Abogunrin F, de Matos Simoes R, Duggan B, Ruddock MW, et al. (2013) Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data. BMC Med 11: 12. doi: 10.1186/1741-7015-11-12 PMID: 23327460
10. Ru Y, Dancik GM, Theodorescu D (2011) Biomarkers for prognosis and treatment selection in advanced bladder cancer patients. Curr Opin Urol 21: 420-427. doi: 10.1097/MOU.0b013e32834956d6 PMID: 21814055
11. Mitra AP, Datar RH, Cote RJ (2005) Molecular staging of bladder cancer. BJU Int 96: 7-12. doi: 10.1111/j.1464-410X.2005.05557.x PMID: 15963111
12. Ewald JA, Downs TM, Cetnar JP, Ricke WA (2013) Expression microarray meta-analysis identifies genes associated with Ras/MAPK and related pathways in progression of muscle-invasive bladder transition cell carcinoma. PLoS One 8: e55414. doi: 10.1371/journal.pone.0055414 PMID: 23383328
13. Mayer P, Mayer B, Mayer G (2012) Systems biology: building a useful model from multiple markers and profiles. Nephrol Dial Transplant 27: 3995-4002. doi: 10.1093/ndt/gfs489 PMID: 23144070
14. Kreeger PK, Lauffenburger DA (2010) Cancer systems biology: a network modeling perspective. Carcinogenesis 31: 2-8. doi: 10.1093/carcin/bgp261 PMID: 19861649
15. Besaratinia A, Cockburn M, Tommasi S (2013) Alterations of DNA methylome in human bladder cancer. Epigenetics 8. doi: 10.4161/epi.25927 PMID: 23975266
16. Chihara Y, Kanai Y, Fujimoto H, Sugano K, Kawashima K, et al. (2013) Diagnostic markers of urothelial cancer based on DNA methylation analysis. BMC Cancer 13: 275. doi: 10.1186/1471-2407-13-275 PMID: 23735005
17. Weiss GJ, Liang WS, Demeure MJ, Kiefer JA, Hostetter G, et al. (2013) A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges. PLoS One 8: e76438. doi: 10.1371/journal.pone.0076438 PMID: 24204627
18. Mischak H, Schanstra JP (2011) CE-MS in biomarker discovery, validation, and clinical application. Proteomics Clin Appl 5: 9-23. doi: 10.1002/prca.201000058 PMID: 21280234
19. Alberice JV, Amaral AFS, Armitage EG, Lorente JA, Algaba F, et al. (2013) Searching for urine biomarkers of bladder cancer recurrence using a liquid chromatography-mass spectrometry and capillary electrophoresis-mass spectrometry metabolomics approach. J Chromatogr A 1318: 163-170. doi: 10.1016/j.chroma.2013.10.002 PMID: 24139504
20. GeneCards (2013) The Human Gene Compendium. Crown Hum Genome Center, Dep Mol Genet Weizmann Inst Sci.
21. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, et al. (2004) ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6: 1-6. doi: 10.1016/S1476-5586(04)80047-2 PMID: 15068665
22. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33: D514-D517. doi: 10.1093/nar/gki033 PMID: 15608251
23. Mayer G, Heinze G, Mischak H, Hellemons ME, Heerspink HJL, et al. (2011) Omics-bioinformatics in the context of clinical data. Methods Mol Biol 719: 479-497. doi: 10.1007/978-1-61779-027-0-22 PMID: 21370098
24. Abu-Asab MS, Chaouchi M, Alesci S, Galli S, Laassri M, et al. (2011) Biomarkers in the age of omics: time for a systems biology approach. OMICS 15: 105-112. doi: 10.1089/omi.2010.0023 PMID: 21319991
25. De Las Rivas J, Fontanillo C (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol 6: e1000807. doi: 10.1371/journal.pcbi.1000807 PMID: 20589078
26. Wixon J, Kell D (2000) The Kyoto encyclopedia of genes and genomes-KEGG. Yeast 17: 48-55.
27. Mi H, Muruganujan A, Thomas PD (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41: D377-86. doi: 10.1093/nar/gks1118 PMID: 23193289
28. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39: D691-D697. doi: 10.1093/nar/gkq1018 PMID: 21067998
29. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, et al. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25: 288-289. doi: 10.1093/bioinformatics/btn615 PMID: 19033274
30. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 41: D991-5. doi: 10.1093/nar/gks1193 PMID: 23193258
31. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, et al. (2013) ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res 41: D987-90. doi: 10.1093/nar/gks1174 PMID: 23193272
32. Maglott D, Ostell J, Pruitt KD, Tatusova T (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35: D26-31. doi: 10.1093/nar/gkl993 PMID: 17148475
33. Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40: D841-6. doi: 10.1093/nar/gkr1088 PMID: 22121220
34. Stark C, Breitkreutz B-J, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39: D698-D704. doi: 10.1093/nar/gkq1116 PMID: 21071413
35. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093. doi: 10.1093/bioinformatics/btp101 PMID: 19237447
36. Bindea G, Galon J, Mlecnik B (2013) CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 29: 661-663. doi: 10.1093/bioinformatics/btt019 PMID: 23325622
37. Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, et al. (2011) A comprehensive proteincentric ID mapping service for molecular data integration. Bioinformatics 27: 1190-1191. doi: 10.1093/bioinformatics/btr101 PMID: 21478197
38. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, et al. (2007) HMDB: the Human Metabolome Database. Nucleic Acids Res 35: D521-6. doi: 10.1093/nar/gkl923 PMID: 17202168
39. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deepsequencing data. Nucleic Acids Res 39: D152-7. doi: 10.1093/nar/gkq1027 PMID: 21037258
40. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-8. doi: 10.1093/nar/gkm952 PMID: 17991681
41. Bernthaler A, Mühlberger I, Fechete R, Perco P, Lukas A, et al. (2009) A dependency graph approach for the analysis of differential gene expression profiles. Mol Biosyst 5: 1720-1731. doi: 10.1039/b903109j PMID: 19585005
42. Rapberger R, Perco P, Sax C, Pangerl T, Siehs C, et al. (2008) Linking the ovarian cancer transcriptome and immunome. BMC Syst Biol 2: 2. doi: 10.1186/1752-0509-2-2 PMID: 18173842
43. Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, et al. (2010) Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med 2: 46ps42. doi: 10.1126/scitranslmed.3001249 PMID: 20739680
44. Vlahou A (2013) Network views for personalized medicine. Proteomics Clin Appl 7: 384-387. doi: 10.1002/prca.201200121 PMID: 23532915
45. Frantzi M, Zerefos PG, Sanchez-Carbayo M, Anagnou NP, Zoidakis J, et al. (2012) Profilin 1 is a Potential Biomarker for Bladder Cancer Aggressiveness. Mol Cell Proteomics 11: M111.009449-M111.009449. doi: 10.1074/mcp.M111.009449 PMID: 22159600
46. Kircher M, Kelso J (2010) High-throughput DNA sequencing-concepts and limitations. Bioessays 32: 524-536. doi: 10.1002/bies.200900181 PMID: 20486139
47. Dakna M, He Z, Yu WC, Mischak H, Kolch W (2009) Technical, bioinformatical and statistical aspects of liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: a critical assessment. J Chromatogr B Analyt Technol Biomed Life Sci 877: 1250-1258. doi: 10.1016/j.jchromb.2008.10.048 PMID: 19010091
48. Frantzi M, Bhat A, Latosinska A (2014) Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 3: 7. doi: 10.1186/2001-1326-3-7 PMID: 24679154
49. Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, et al. (2003) Pathways database system: an integrated system for biological pathways. Bioinformatics 19: 930-937. doi: 10.1093/bioinformatics/btg113 PMID: 12761054
50. Stein LD (2003) Integrating biological databases. Nat Rev Genet 4: 337-345. doi: 10.1038/nrg1065 PMID: 12728276
51. Philippi S, Köhler J (2006) Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet 7: 482-488. doi: 10.1038/nrg1872 PMID: 16682980
52. Comprehensive molecular characterization of urothelial bladder carcinoma. (2014). Nature 507: 315-322. doi: 10.1038/nature12965 PMID: 24476821
53. Wu X-R (2005) Urothelial tumorigenesis: a tale of divergent pathways. Nat Rev Cancer 5: 713-725. doi: 10.1038/nrc1697 PMID: 16110317
54. McConkey DJ, Lee S, Choi W, Tran M, Majewski T, et al. (2010) Molecular genetics of bladder cancer: Emerging mechanisms of tumor initiation and progression. Urol Oncol 28: 429-440. doi: 10.1016/j. urolonc.2010.04.008 PMID: 20610280
55. Reichardt LF (2006) Neurotrophin-regulated signalling pathways. Philos Trans R Soc Lond B Biol Sci 361: 1545-1564. doi: 10.1098/rstb.2006.1894 PMID: 16939974
56. Thiele CJ, Li Z, McKee AE (2009) On Trk-the TrkB signal transduction pathway is an increasingly important target in cancer biology. Clin Cancer Res 15: 5962-5967. doi: 10.1158/1078-0432.CCR-08-0651 PMID: 19755385
57. Koochekpour S (2010) Androgen receptor signaling and mutations in prostate cancer. Asian J Androl 12: 639-657. doi: 10.1038/aja.2010.89 PMID: 20711217
58. Assimakopoulou M, Kondyli M, Gatzounis G, Maraziotis T, Varakis J (2007) Neurotrophin receptors expression and JNK pathway activation in human astrocytomas. BMC Cancer 7: 202. doi: 10.1186/1471-2407-7-202 PMID: 17971243
59. Mosesson Y, Mills GB, Yarden Y (2008) Derailed endocytosis: an emerging feature of cancer. Nat Rev Cancer 8: 835-850. doi: 10.1038/nrc2521 PMID: 18948996
60. Polo S, Pece S, Di Fiore PP (2004) Endocytosis and cancer. Curr Opin Cell Biol 16: 156-161. doi: 10.1016/j.ceb.2004.02.003 PMID: 15196558
61. Karam JA, Shariat SF, Huang H-Y, Pong R-C, Ashfaq R, et al. (2007) Decreased DOC-2/DAB2 expression in urothelial carcinoma of the bladder. Clin Cancer Res 13: 4400-4406. doi: 10.1158/1078-0432.CCR-07-0287 PMID: 17671122
62. Price LS, Collard JG (2001) Regulation of the cytoskeleton by Rho-family GTPases: implications for tumour cell invasion. Semin Cancer Biol 11: 167-173. doi: 10.1006/scbi.2000.0367 PMID: 11322835
63. Yu L, Yuan X, Wang D, Barakat B, Williams ED, et al. (2014) Selective regulation of p38β protein and signaling by integrin-linked kinase mediates bladder cancer cell migration. Oncogene 33: 690-701. doi: 10.1038/onc.2013.20 PMID: 23435415
64. Yuan X, Yu L, Li J, Xie G, Rong T, et al. (2013) ATF3 suppresses metastasis of bladder cancer by regulating gelsolin-mediated remodeling of the actin cytoskeleton. Cancer Res 73: 3625-3637. doi: 10.1158/0008-5472.CAN-12-3879 PMID: 23536558
65. Kamai T, Tsujii T, Arai K, Takagi K, Asami H, et al. (2003) Significant association of Rho/ROCK pathway with invasion and metastasis of bladder cancer. Clin Cancer Res 9: 2632-2641. PMID: 12855641