Proteome-wide discovery of mislocated proteins in cancer

Genome Research

Volumn 23, Issue 8, 2013, Pages 1283-1294

  Lee, KiYoung ^a   Byun, Kyunghee ^b   Hong, Wonpyo ^a   Chuang, Han Yu ^c   Pack, Chan Gi ^d   Bayarsaikhan, Enkhjargal ^b   Paek, Sun Ha ^e   Kim, Hyosil ^a   Shin, Hye Young ^e   Ideker, Trey ^c   Lee, Bonghee ^b  

^a Ajou University School of Medicine   (South Korea)

^b Gachon University College of Medicine   (South Korea)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d RIKEN   (Japan)

^e Seoul National University College of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

GLIAL CELL LINE DERIVED NEUROTROPHIC FACTOR; PERSEPHIN; PROTEIN; PROTEIN GFRA4; PROTEIN NFRKB; PROTEIN RNF138; PROTEIN TLX3; PROTEOME; STAT3 PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CELL MEMBRANE; CELL NUCLEUS; CELL PROLIFERATION; ENDOPLASMIC RETICULUM; EXON; GENE EXPRESSION; GLIOMA; GLIOMA CELL; HUMAN; IMMUNOFLUORESCENCE; NEOPLASM; POINT MUTATION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; WESTERN BLOTTING;

EID: 84881174691     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.155499.113     Document Type: Article

References (57)

1. Bacia K, Kim SA, Schwille P. 2006. Fluorescence cross-correlation spectroscopy in living cells. Nat Methods 3: 83-89.
2. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. 2001. BIND - the Biomolecular Interaction Network Database. Nucleic Acids Res 29: 242-245.
3. Bhasin M, Raghava GP. 2004. ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res 32: W414-W419.
4. Chen Y, Xu D. 2004. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res 32: 6414-6424.
5. Chou KC, Cai YD. 2005. Predicting protein localization in budding yeast. Bioinformatics 21: 944-950.
6. Costa BM, Smith JS, Chen Y, Chen J, Phillips HS, Aldape KD, Zardo G, Nigro J, James CD, Fridlyand J, et al. 2010. Reversing HOXA9 oncogene activation by PI3K inhibition: Epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res 70: 453-462.
7. Dodt G, Braverman N, Wong C, Moser A, Moser HW, Watkins P, Valle D, Gould SJ. 1995. Mutations in the PTS1 receptor gene, PXR1, define complementation group 2 of the peroxisome biogenesis disorders. Nat Genet 9: 115-125.
8. Dubois D, Foulloy L, Mauris G, Prade H. 2004. Probability-possibility transformations, triangular fuzzy sets, and probabilistic inequalities. Reliable Computing 10: 273-297.
9. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, et al. 2007. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 3: 89.
10. Gardy JL, Spencer C,Wang K, Ester M, Tusnady GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, et al. 2003. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 31: 3613-3617.
11. Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Gosline SJ, Hallett M, et al. 2006. Quantitative proteomics analysis of the secretory pathway. Cell 127: 1265-1281.
12. Hansford JR, Mulligan LM. 2000. Multiple endocrine neoplasia type 2 and RET: From neoplasia to neurogenesis. J Med Genet 37: 817-827.
13. Herrmann JM, Riemer J. 2010. Oxidation and reduction of cysteines in the intermembrane space of mitochondria: Multiple facets of redox control. Antioxid Redox Signal 13: 1323-1326.
14. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. 2007. WoLF PSORT: Protein localization predictor. Nucleic Acids Res 35: W585-W587.
15. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW,Weissman JS, O'Shea EK. 2003. Global analysis of protein localization in budding yeast. Nature 425: 686-691.
16. Jiang JQ, Wu M. 2012. Predicting multiplex subcellular localization of proteins using protein-protein interaction network: A comparative study. BMC Bioinformatics (Suppl 10) 13: S20.
17. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. 2005. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res 33: D428-D432.
18. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. 2004. Whole-genome annotation by using evidence integration in functionallinkage networks. Proc Natl Acad Sci 101: 2888-2893.
19. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. 2009. Human Protein Reference Database - 2009 update. Nucleic Acids Res 37: D767-D772.
20. Khatua S, Peterson KM, Brown KM, Lawlor C, Santi MR, LaFleur B, Dressman D, Stephan DA, MacDonald TJ. 2003. Overexpression of the EGFR/ FKBP12/HIF-2a pathway identified in childhood astrocytomas by angiogenesis gene profiling. Cancer Res 63: 1865-1870.
21. Lee K, Kim DW, Na D, Lee KH, Lee D. 2006. PLPD: Reliable protein localization prediction from imbalanced and overlapped datasets. Nucleic Acids Res 34: 4655-4666.
22. Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. 2008. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 36: E136.
23. Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. 2010. Mapping plant interactomes using literature curated and predicted proteinprotein interaction data sets. Plant Cell 22: 997-1005.
24. Liang WS, Dunckley T, Beach TG, Grover A, Mastroeni D,Walker DG, Caselli RJ, KukullWA, McKeel D, Morris JC, et al. 2007. Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain. Physiol Genomics 28: 311-322.
25. Lin LF, Doherty DH, Lile JD, Bektesh S, Collins F. 1993. GDNF: A glial cell line-derived neurotrophic factor for midbrain dopaminergic neurons. Science 260: 1130-1132.
26. Lindahl M, Poteryaev D, Yu L, Arumae U, Timmusk T, Bongarzone I, Aiello A, Pierotti MA, Airaksinen MS, Saarma M. 2001. Human glial cell linederived neurotrophic factor receptor a 4 is the receptor for persephin and is predominantly expressed in normal and malignant thyroid medullary cells. J Biol Chem 276: 9344-9351.
27. Lockstone HE, Harris LW, Swatton JE, Wayland MT, Holland AJ, Bahn S. 2007. Gene expression profiling in the adult Down syndrome brain. Genomics 90: 647-660.
28. Marucci G, Morandi L, Magrini E, Farnedi A, Franceschi E,Miglio R, Calo D, Pession A, Foschini MP, Eusebi V. 2008. Gene expression profiling in glioblastoma and immunohistochemical evaluation of IGFBP-2 and CDC20. Virchows Arch 453: 599-609.
29. Massague J. 1998. TGF-b signal transduction. Annu Rev Biochem 67: 753-791.
30. Milbrandt J, de Sauvage FJ, Fahrner TJ, Baloh RH, Leitner ML, Tansey MG, Lampe PA, Heuckeroth RO, Kotzbauer PT, Simburger KS, et al. 1998. Persephin, a novel neurotrophic factor related to GDNF and neurturin. Neuron 20: 245-253.
31. Mintz-Oron S, Aharoni A, Ruppin E, Shlomi T. 2009. Network-based prediction ofmetabolic enzymes' subcellular localization. Bioinformatics 25: i247-i252.
32. Mott R, Schultz J, Bork P, Ponting CP. 2002. Predicting protein cellular localization using a domain projection method. Genome Res 12: 1168-1174.
33. Mulligan LM, Eng C, Healey CS, Clayton D, Kwok JB, Gardner E, Ponder MA, Frilling A, Jackson CE, Lehnert H, et al. 1994. Specific mutations of the RET proto-oncogene are related to disease phenotype in MEN 2A and FMTC. Nat Genet 6: 70-74.
34. Munkres KD, Benveniste K, Gorski J, Zuiches CA. 1970. Genetically induced subcellular mislocation of Neurospora mitochondrial malate dehydrogenase. Proc Natl Acad Sci 67: 263-270.
35. Nakao A, Imamura T, Souchelnytskyi S, Kawabata M, Ishisaki A, Oeda E, Tamaki K, Hanai J, Heldin CH, Miyazono K, et al. 1997. TGF-b receptormediated signalling through Smad2, Smad3 and Smad4. EMBO J 16: 5353-5362.
36. Noda Y, Horikawa S, Kanda E, Yamashita M, Meng H, Eto K, Li Y, Kuwahara M, Hirai K, Pack C, et al. 2008. Reciprocal interaction with G-Actin and tropomyosin is essential for aquaporin-2 trafficking. J Cell Biol 182: 587-601.
37. Obozinski G, Lanckriet G, Grant C, Jordan MI, Noble WS. 2008. Consistent probabilistic outputs for protein function prediction. Genome Biol (Suppl 1) 9: S6.
38. Owen LA, Kowalewski AA, Lessnick SL. 2008. EWS/FLI mediates transcriptional repression via NKX2.2 during oncogenic transformation in Ewing's sarcoma. PloS one 3: E1965.
39. Pack C, Saito K, Tamura M, Kinjo M. 2006. Microenvironment and effect of energy depletion in the nucleus analyzed by mobility of multiple oligomeric EGFPs. Biophys J 91: 3921-3936.
40. Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, et al. 2008. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (Suppl 1) 9: S2.
41. Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
42. Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM. 2005. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 6: R40.
43. Reich NC, Liu L. 2006. Tracking STAT nuclear traffic. Nat Rev Immunol 6: 602-612.
44. Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L, et al. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402: 413-418.
45. Rossel M, Pasini A, Chappuis S, Geneste O, Fournier L, Schuffenecker I, Takahashi M, van Grunsven LA, Urdiales JL, Rudkin BB, et al. 1997. Distinct biological properties of two RET isoforms activated by MEN 2A and MEN 2B mutations. Oncogene 14: 265-275.
46. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, et al. 2005. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
47. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. 2004. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-D451.
48. Scott MS, Thomas DY, Hallett MT. 2004. Predicting subcellular localization via protein motif co-occurrence. Genome Res 14: 1957-1966.
49. Shatkay H, Hoglund A, Brady S, Blum T, Donnes P, Kohlbacher O. 2007. SherLoc: High-Accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 23: 1410-1417.
50. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al. 2005. A human protein-protein interaction network: A resource for annotating the proteome. Cell 122: 957-968.
51. Sun Y, Liu X, Eaton EN, Lane WS, Lodish HF,Weinberg RA. 1999. Interaction of the Ski oncoprotein with Smad3 regulates TGF-b signaling. Mol Cell 4: 499-509.
52. Uehara T, Nakamura T, Yao D, Shi ZQ, Gu Z, Ma Y, Masliah E, Nomura Y, Lipton SA. 2006. S-nitrosylated protein-disulphide isomerase links protein misfolding to neurodegeneration. Nature 441: 513-517.
53. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, et al. 2010. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 28: 1248-1250.
54. Vascotto C, Bisetto E, Li M, Zeef LA, D'Ambrosio C, Domenis R, Comelli M, Delneri D, Scaloni A, Altieri F, et al. 2011. Knock-in reconstitution studies reveal an unexpected role of Cys-65 in regulating APE1/Ref-1 subcellular trafficking and function. Mol Biol Cell 22: 3887-3901.
55. Wickner W, Schekman R. 2005. Protein translocation across biological membranes. Science 310: 1452-1456.
56. Wilson CA, Kreychman J, Gerstein M. 2000. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 297: 233-249.
57. Zhou B, Bae SK, Malone AC, Levinson BB, Kuo YM, Cilio MR, Bertini E, Hayflick SJ, Gitschier JM. 2001. hGFRa-4: A new member of the GDNF receptor family and a candidate for NBIA. Pediatr Neurol 25: 156-161.