Analysis of protein-protein interactions in cross-talk pathways reveals CRKL protein as a novel prognostic marker in hepatocellular carcinoma

Molecular and Cellular Proteomics

Volumn 12, Issue 5, 2013, Pages 1335-1349

  Liu, Chia Hung ^a   Chen, Tzu Chi ^b   Chau, Gar Yang ^c   Jan, Yi Hua ^d   Chen, Chun Houh ^e   Hsu, Chun Nan ^f,g   Lin, Kuan Ting ^b   Juang, Yue Li ^h   Lu, Pei Jung ⁱ   Cheng, Hui Chuan ⁱ   Chen, Ming Huang ^b   Chang, Chia Fen ^b   Ting, Yu Shan ^b   Kao, Cheng Yan ^a   Hsiao, Michael ^d   Huang, Chi Ying F ^b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c TAIPEI VETERANS GENERAL HOSPITAL   (Taiwan)

^d GENOMICS RESEARCH CENTER   (Taiwan)

^e INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^f INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^g UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^h TZU CHI UNIVERSITY   (Taiwan)

ⁱ NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CRK LIKE PROTEIN; VASCULOTROPIN RECEPTOR 1;

ADULT; ARTICLE; CANCER CELL; CANCER PATIENT; CANCER PROGNOSIS; CANCER SURVIVAL; CONTROLLED STUDY; FEMALE; HUMAN; HUMAN CELL; IMMUNOHISTOCHEMISTRY; LIVER CELL CARCINOMA; MAJOR CLINICAL STUDY; MALE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ADULT; AGED; AGED, 80 AND OVER; CARCINOMA, HEPATOCELLULAR; DISEASE-FREE SURVIVAL; HEK293 CELLS; HEP G2 CELLS; HUMANS; KAPLAN-MEIER ESTIMATE; LIVER NEOPLASMS; MIDDLE AGED; NUCLEAR PROTEINS; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; PROTEIN INTERACTION MAPS; RETROSPECTIVE STUDIES; SIGNAL TRANSDUCTION; TISSUE ARRAY ANALYSIS; TUMOR MARKERS, BIOLOGICAL; VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR-1; YOUNG ADULT;

EID: 84877611417     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O112.020404     Document Type: Article

References (45)

1. Jemal, A., Siegel, R., Ward, E., Hao, Y., Xu, J., Murray, T., and Thun, M. J. (2008) Cancer Statistics, 2008. CA-Cancer J. Clin. 58, 71-96 (Pubitemid 351521864)
2. Whittaker, S., Marais, R., and Zhu, A. X. (2010) The role of signaling pathways in the development and treatment of hepatocellular carcinoma. Oncogene 29, 4989-5005
3. Barabási, A.-L., Gulbahce, N., and Loscalzo, J. (2011) Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12, 56-68
4. Taylor, I. W., Linding, R., Warde-Farley, D., Liu, Y., Pesquita, C., Faria, D., Bull, S., Pawson, T., Morris, Q., and Wrana, J. L. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat. Biotechnol. 27, 199-204
5. Chuang, H.-Y., Lee, E., Liu, Y.-T., Lee, D., and Ideker, T. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140
6. Hanahan, D., and Weinberg, R. A. (2011) Hallmarks of cancer: the next generation. Cell 144, 646-674
7. Vogelstein, B., and Kinzler, K. W. (2004) Cancer genes and the pathways they control. Nat. Med. 10, 789-799 (Pubitemid 39070849)
8. Sawyers, C. (2004) Targeted cancer therapy. Nature 432, 294-297
9. Hopkins, A. L. (2008) Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 4, 682-690
10. Llovet, J. M., and Bruix, J. (2008) Molecular targeted therapies in hepatocellular carcinoma. Hepatology 48, 1312-1327
11. Söderberg, O., Gullberg, M., Jarvius, M., Ridderstråle, K., Leuchowius, K. J., Jarvius, J., Wester, K., Hydbring, P., Bahram, F., Larsson, L. G., and Landegren, U. (2006) Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods 3, 995-1000 (Pubitemid 44782698)
12. Ahmad, S., Alsayed, Y. M., Druker, B. J., and Platanias, L. C. (1997) The type I interferon receptor mediates tyrosine phosphorylation of the CrkL adaptor protein. J. Biol. Chem. 272, 29991-29994 (Pubitemid 27512190)
13. Smit, L., van der Horst, G., and Borst, J. (1996) Sos, Vav, and C3G participate in B cell receptor-induced signaling pathways and differentially associate with Shc-Grb2, Crk, and Crk-L adaptors. J. Biol. Chem. 271, 8564-8569
14. Feller, S. M. (2001) Crk family adaptors-signalling complex formation and biological roles. Oncogene 20, 6348-6371
15. Kim, Y. H., Kwei, K. A., Girard, L., Salari, K., Kao, J., Pacyna-Gengelbach, M., Wang, P., Hernandez-Boussard, T., Gazdar, A. F., Petersen, I., Minna, J. D., and Pollack, J. R. (2010) Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer. Oncogene 29, 1421-1430
16. Barleon, B., Sozzani, S., Zhou, D., Weich, H. A., Mantovani, A., and Marmé, D. (1996) Migration of human monocytes in response to vascular endothelial growth factor (VEGF) is mediated via the VEGF receptor flt-1. Blood 87, 3336-3343 (Pubitemid 26115364)
17. Kanno, S., Oda, N., Abe, M., Terai, Y., Ito, M., Shitara, K., Tabayashi, K., Shibuya, M., and Sato, Y. (2000) Roles of two VEGF receptors, Flt-1 and KDR, in the signal transduction of VEGF effects in human vascular endothelial cells. Oncogene 19, 2138-2146 (Pubitemid 30251379)
18. Hsu, C. N., Lai, J. M., Liu, C. H., Tseng, H. H., Lin, C. Y., Lin, K. T., Yeh, H. H., Sung, T. Y., Hsu, W. L., Su, L. J., Lee, S. A., Chen, C. H., Lee, G. C., Lee, D. T., Shiue, Y. L., Yeh, C. W., Chang, C. H., Kao, C. Y., and Huang, C. Y. (2007) Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma Genes Online). BMC Bioinformatics 8, 66
19. Chen, M. H., Yang, W. L., Lin, K. T., Liu, C. H., Liu, Y. W., Huang, K. W., Chang, P. M., Lai, J. M., Hsu, C. N., Chao, K. M., Kao, C. Y., and Huang, C. Y. (2011) Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma. PLoS ONE 6, e27186
20. Kamburov, A., Stelzl, U., Lehrach, H., and Herwig, R. (2012) The ConsensusPathDB Interaction Database: 2013 update. Nucleic Acids Res., 41, D793-800
21. Lee, S. A., Chan, C. H., Chen, T. C., Yang, C. Y., Huang, K. C., Tsai, C. H., Lai, J. M., Wang, F. S., Kao, C. Y., and Huang, C. Y. (2009) POINeT: protein interactome with sub-network analysis and hub prioritization. BMC Bioinformatics 10, 114
22. McDowall, M. D., Scott, M. S., and Barton, G. J. (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res. 37, D651-D656
23. Jarvius, M., Paulsson, J., Weibrecht, I., Leuchowius, K.-J., Andersson, A.-C., Wählby, C., Gullberg, M., Botling, J., Sjöblom, T., Markova, B., Ostman, A., Landegren, U., and Söderberg, O. (2007) In situ detection of phosphorylated platelet-derived growth factor receptor using a generalized proximity ligation method. Mol. Cell. Proteomics 6, 1500-1509 (Pubitemid 47506163)
24. Chen, C. H. (2002) Generalized association plots: Information visualization via iteratively generated correlation matrices. Statistica Sinica 12, 7-30
25. Wu, H. M., Tien, Y. J., and Chen, C. (2010) GAP: A graphical environment for matrix visualization and cluster analysis. Computational Statistics & Data Analysis 54, 767-778
26. Deleted in proof
27. Jonsson, P. F., and Bates, P. A. (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22, 2291-2297 (Pubitemid 44390886)
28. Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabási, A. L. (2007) The human disease network. Proc. Natl. Acad. Sci. U.S.A. 104, 8685-8690 (Pubitemid 47175372)
29. Ideker, T., and Krogan, N. J. (2012) Differential network biology. Mol. Syst. Biol. 8, 565
30. Bandyopadhyay, S., Mehta, M., Kuo, D., Sung, M. K., Chuang, R., Jaehnig, E. J., Bodenmiller, B., Licon, K., Copeland, W., and Shales, M., Fiedler, D., Dutkowski, J., Guénolé, A, van Attikum, H., Shokat, K. M., Kolodner, R. D., Huh, W. K., Aebersold, R., Keogh, M. C., Krogan, N. J., and Ideker, T. (2010) Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389
31. Thomas, M. B., Morris, J. S., Chadha, R., Iwasaki, M., Kaur, H., Lin, E., Lin, E., Kaseb, A., Glover, K., Davila, M., and Abbruzzese, J. (2009) Phase II trial of the combination of bevacizumab and erlotinib in patients who have advanced hepatocellular carcinoma. J. Clin. Oncol. 27, 843-850
32. Barabási, A. L., and Oltvai, Z. N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113
33. Kaplan, R. N., Riba, R. D., Zacharoulis, S., Bramley, A. H., Vincent, L., Costa, C., MacDonald, D. D., Jin, D. K., Shido, K., and Kerns, S. A., Zhu, Z., Hicklin, D., Wu, Y., Port, J. L., Altorki, N., Port, E. R., Ruggero, D., Shmelkov, S. V., Jensen, K. K., Rafii, S., and Lyden, D. (2005) VEGFR1-positive haematopoietic bone marrow progenitors initiate the pre-metastatic niche. Nature 438, 820-827 (Pubitemid 41753060)
34. Sriram, G., and Birge, R. B. (2010) Emerging roles for Crk in human cancer. Genes Cancer 1, 1132-1139
35. Johannessen, C. M., Boehm, J. S., Kim, S. Y., Thomas, S. R., Wardwell, L., Johnson, L. A., Emery, C. M., Stransky, N., Cogdill, A. P., Barretina, J., Caponigro, G., Hieronymus, H., Murray, R. R., Salehi-Ashtiani, K., Hill, D. E., Vidal, M., Zhao, J. J., Yang, X., Alkan, O., Kim, S., Harris, J. L., Wilson, C. J., Myer, V. E., Finan, P. M., Root, D. E., Roberts, T. M., Golub, T., Flaherty, K. T., Dummer, R., Weber, B. L., Sellers, W. R., Schlegel, R., Wargo, J. A., Hahn, W. C., and Garraway, L. A. (2010) COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature 468, 968-972
36. Cheung, H.W., Du, J., Boehm, J. S., He, F., Weir, B. A., Wang, X., Butaney, M., Sequist, L. V., Luo, B., Engelman, J. A., Root, D. E., Meyerson, M., Golub, T. R., Jänne, P. A., and Hahn, W. C. (2011) Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers. Cancer Discovery, 1, 608-625
37. Chiu, S. T., Chang, K. J., Ting, C. H., Shen, H. C., Li, H., and Hsieh, F. J. (2009) Over-expression of EphB3 enhances cell-cell contacts and suppresses tumor growth in HT-29 human colon cancer cells. Carcinogenesis 30, 1475-1486
38. Shen, Q., Rahn, J. J., Zhang, J., Gunasekera, N., Sun, X., Shaw, A. R., Hendzel, M. J., Hoffman, P., Bernier, A., and Hugh, J. C. (2008) MUC1 initiates Src-CrkL-Rac1/Cdc42-mediated actin cytoskeletal protrusive motility after ligating intercellular adhesion molecule-1. Mol. Cancer Res. 6, 555-567 (Pubitemid 351521837)
39. Kobashigawa, Y., and Inagaki, F. (2012) Structural biology: CrkL is not Crk-like. Nat. Chem. Biol. 8, 504-505
40. Guiet, R., Van Goethem, E., Cougoule, C., Balor, S., Valette, A., Al Saati, T., Lowell, C. A., Le Cabec, V., and Maridonneau-Parini, I. (2011) The process of macrophage migration promotes matrix metalloproteinase-independent invasion by tumor cells. J. Immunol. 187, 3806-3814
41. Hemmeryckx, B., van Wijk, A., Reichert, A., Kaartinen, V., de Jong, R., Pattengale, P. K., Gonzalez-Gomez, I., Groffen, J., and Heisterkamp, N. (2001) Crkl enhances leukemogenesis in BCR/ABL P190 transgenic mice. Cancer Res. 61, 1398-1405 (Pubitemid 34292563)
42. Fan, F., Wey, J. S., McCarty, M. F., Belcheva, A., Liu, W., Bauer, T. W., Somcio, R. J., Wu, Y., Hooper, A., Hicklin, D. J., and Ellis, L. M. (2005) Expression and function of vascular endothelial growth factor receptor-1 on human colorectal cancer cells. Oncogene 24, 2647-2653 (Pubitemid 40593092)
43. Wey, J. S., Fan, F., Gray, M. J., Bauer, T. W., McCarty, M. F., Somcio, R., Liu, W., Evans, D. B., Wu, Y., Hicklin, D. J., and Ellis, L. M. (2005) Vascular endothelial growth factor receptor-1 promotes migration and invasion in pancreatic carcinoma cell lines. Cancer 104, 427-438 (Pubitemid 40993273)
44. Li, T., Zhu, Y., Ren, W., Xu, S., Yang, Z., Fang, A., and Qin, C. (2012) High co-expression of vascular endothelial growth factor receptor-1 and Snail is associated with poor prognosis after curative resection of hepatocellular carcinoma. Med. Oncol. 29(4), 2750-2761
45. Villanueva, A., Hoshida, Y., Toffanin, S., Lachenmayer, A., Alsinet, C., Savic, R., Cornella, H., and Llovet, J. M. (2010) New strategies in hepatocellular carcinoma: genomic prognostic markers. Clin. Cancer Res. 16, 4688-4694