Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2805-2817

  Zhang, Emma Yue ^a   Cristofanilli, Massimo ^b,c   Robertson, Fredika ^d   Reuben, James M ^c,d   Mu, Zhaomei ^b   Beavis, Ronald C ^e   Im, Hogune ^f   Snyder, Michael ^f   Hofree, Matan ^g   Ideker, Trey ^g   Omenn, Gilbert S ^h   Fanayan, Susan ⁱ   Jeong, Seul Ki ^j   Paik, Young Ki ^j   Zhang, Anna Fan ^a   Wu, Shiaw Lin ^a   Hancock, William S ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^d UNIVERSITY OF TEXAS   (United States)

^e UNIVERSITY OF MANITOBA   (Canada)

^f STANFORD UNIVERSITY   (United States)

^g UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^h UNIVERSITY OF MICHIGAN   (United States)

ⁱ MACQUARIE UNIVERSITY   (Australia)

^j Yonsei University   (South Korea)

more..

Author keywords

Chromosome centric Human Proteome Project; EGFR; ERBB2; Inflammatory breast cancer

Indexed keywords

CARBAMOYL PHOSPHATE SYNTHASE; CATENIN; CAVEOLIN 1; CRK LIKE PROTEIN; EPHRIN RECEPTOR A2; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; FILAMIN A; GROWTH FACTOR RECEPTOR BOUND PROTEIN 2; MYC PROTEIN; NUCLEOLIN; PHOSPHATIDYLINOSITOL 3 KINASE; PLECTIN; PROTEIN P53; PROTEIN S 100; S100 A2 PROTEIN; SERPIN B5; STRATIFIN; TRANSFERRIN RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; GENE EXPRESSION; GENE INTERACTION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; INFLAMMATORY BREAST CANCER; ONCOGENE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEOMICS; RNA SEQUENCE; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; TRANSCRIPTOMICS;

EID: 84879327240     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4001527     Document Type: Article

References (57)

1. Mortazavi, A.; Williams, B. A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 2008, 5 (7) 621-8
2. Yang, Z.; Harris, L. E.; Palmer-Toy, D. E.; Hancock, W. S. Multilectin affinity chromatography for characterization of multiple glycoprotein biomarker candidates in serum from breast cancer patients Clin. Chem. 2006, 52 (10) 1897-905
3. Zeng, Z.; Hincapie, M.; Haab, B. B.; Hanash, S.; Pitteri, S. J.; Kluck, S.; Hogan, J. M.; Kennedy, J.; Hancock, W. S. The development of an integrated platform to identify breast cancer glycoproteome changes in human serum J. Chromatogr., A 2010, 1217 (19) 3307-15
4. Zeng, Z.; Hincapie, M.; Pitteri, S. J.; Hanash, S.; Schalkwijk, J.; Hogan, J. M.; Wang, H.; Hancock, W. S. A proteomics platform combining depletion, multi-lectin affinity chromatography (M-LAC), and isoelectric focusing to study the breast cancer proteome Anal. Chem. 2011, 83 (12) 4845-54
5. Forozan, F.; Veldman, R.; Ammerman, C.; Parsa, N.; Kallioniemi, A.; Kallioniemi, O.-P.; Ethier, S. Molecular cytogenetic analysis of 11 new breast cancer cell lines Br. J. Cancer 1999, 81 (8) 7
6. Liang, Z.; Zeng, X.; Gao, J.; Wu, S.; Wang, P.; Shi, X.; Zhang, J.; Li, T. Analysis of EGFR, HER2, and TOP2A gene status and chromosomal polysomy in gastric adenocarcinoma from Chinese patients BMC Cancer 2008, 8 (363) 12
7. Mendelsohn, J.; Baselga, J. The EGF receptor family as targets for cancer therapy Oncogene 2000, 19 (56) 16
8. Ross, J. S.; Fletcher, J. A. The HER-2/neu oncogene: prognostic factor, predictive factor and target for therapy Semin. Cancer Biol. 1999, 9 (2) 125-38
9. Kauraniemi, P.; Hautaniemi, S.; Autio, R.; Astola, J.; Monni, O.; Elkahloun, A.; Kallioniemi, A. Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines Oncogene 2004, 23 (4) 1010-3
10. Wu, S.-L.; Kim, J.; Bandle, R. W.; Liotta, L.; Petricoin, E.; Karger, B. L. Dynamic profiling of the post-translational modifications and interaction partners of epidermal growth factor receptor signaling after stimulation by epidermal growth factor using extended range proteomic analysis (ERPA) Mol. Cell. Proteomics 2006, 5 (9) 18
11. Ahn, E. R.; Vogel, C. L. Dual HER2-targeted approaches in HER2-positive breast cancer Breast Cancer Res. Treat. 2012, 131 (2) 371-83
12. Harris, L.; Fritsche, H.; Menne, R.; Norton, L.; Ravdin, P.; Sheila, T.; Somerfield, M. R.; Hayes, D. F.; Bast, R. C., Jr American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer J. Clin. Oncol. 2007, 25 (33) 5287-5312
13. Choi, H.; Fermin, D.; Nesvizhskii, A. I. Significance analysis of spectral count data in label-free shotgun proteomics Mol. Cell. Proteomics 2008, 7 (12) 2373-85
14. Ferguson, R. E.; Carroll, H. P.; Harris, A.; Maher, E. R.; Selby, P. J.; Banks, R. E. Housekeeping proteins: A preliminary study illustrating some limitations as useful references in protein expression studies Proteomics 2005, 5, 6
15. Zhang, L.; Li, W.-H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes Mol. Biol. Evol. 2004, 21 (2) 4
16. Chen, R.; Mias, G. I.; Li-Pook-Than, J.; Jiang, L.; Lam, H. Y.; Miriami, E.; Karczewski, K. J.; Hariharan, M.; Dewey, F. E.; Cheng, Y.; Clark, M. J.; Im, H.; Habegger, L.; Balasubramanian, S.; O'Huallachain, M.; Dudley, J. T.; Hillenmeyer, S.; Haraksingh, R.; Sharon, D.; Euskirchen, G.; Lacroute, P.; Bettinger, K.; Boyle, A. P.; Kasowski, M.; Grubert, F.; Seki, S.; Garcia, M.; Whirl-Carrillo, M.; Gallardo, M.; Blasco, M. A.; Greenberg, P. L.; Snyder, P.; Klein, T. E.; Altman, R. B.; Butte, A. J.; Ashley, E. A.; Gerstein, M.; Nadeau, K. C.; Tang, H.; Snyder, M. Personal omics profiling reveals dynamic molecular and medical phenotypes Cell 2012, 148 (6) 1293-307
17. Orazine, C. I.; Hincapie, M.; Hancock, W. S.; Hattersley, M.; Hanke, J. H. A proteomic analysis of the plasma glycoproteins of a MCF-7 mouse xenograft: a model system for the detection of tumor markers J. Proteome Res. 2008, 7 (4) 1542-54
18. Wu, S. L.; Hancock, W. S.; Goodrich, G. G.; Kunitake, S. T. An approach to the proteomic analysis of a breast cancer cell line (SKBR-3) Proteomics 2003, 3 (6) 1037-46
19. Wu, S. L.; Taylor, A. D.; Lu, Q.; Hanash, S. M.; Im, H.; Snyder, M.; Hancock, W. S. Identification of potential glycan cancer markers with sialic acid attached to sialic acid and up-regulated fucosylated galactose structures in epidermal growth factor receptor secreted from A431 cell line Mol. Cell. Proteomics 2013, 12 (5) 1239-49
20. Paik, Y. K.; Hancock, W. S. Uniting ENCODE with genome-wide proteomics Nat. Biotechnol. 2012, 30 (11) 1065-7
21. Greenbaum, D.; Colangelo, C.; Williams, K.; Gerstei, M. Comparing protein abundance and mRNA expression levels on a genomic scale Genome Biol. 2003, 4 (9) 117
22. Lev, D.; Kim, L.; Melnikova, V.; Ruiz, M.; Ananthaswamy, H.; Price, J. Dual blockade of EGFR and ERK1/2 phosphorylation potentiates growth inhibition of breast cancer cells Br. J. Cancer 2004, 91 (4) 8
23. Zhang, C.-C.; Rogalski, J. C.; Evans, D. M.; Klockenbusch, C.; Beavis, R. C.; Kast, J. In silico protein interaction analysis using the global proteome machine database J. Proteome Res. 2011, 10 (2) 13
24. Bignell, G. R.; Santarius, T.; Pole, J. C.; Butler, A. P.; Perry, J.; Pleasance, E.; Greenman, C.; Menzies, A.; Taylor, S.; Edkins, S.; Campbell, P.; Quail, M.; Plumb, B.; Matthews, L.; McLay, K.; Edwards, P. A.; Rogers, J.; Wooster, R.; Futreal, P. A.; Stratton, M. R. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution Genome Res. 2007, 17 (9) 1296-303
25. Ethier, S. P. Identifying and validating causal genetic alterations in human breast cancer Breast Cancer Res. Treat. 2003, 78 (3) 285-7
26. Johnson, G. R.; Kannan, B.; Shoyab, M.; Stromberg, K. Amphiregulin induces tyrosine phosphorylation of the epidermal growth factor receptor and p185erbB2. Evidence that amphiregulin acts exclusively through the epidermal growth factor receptor at the surface of human epithelial cells J. Biol. Chem. 1993, 268 (4) 2924-31
27. Franklin, M. C.; Carey, K. D.; Vajdos, F. F.; Leahy, D. J.; de Vos, A. M.; Sliwkowski, M. X. Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex Cancer Cell 2004, 5 (4) 317-28
28. Hudelist, G.; Singer, C. F.; Manavi, M.; Pischinger, K.; Kubista, E.; Czerwenka, K. Co-expression of ErbB-family members in human breast cancer: Her-2/neu is the preferred dimerization candidate in nodal-positive tumors Breast Cancer Res. Treat. 2003, 80 (3) 353-61
29. Holbro, T.; Beerli, R. R.; Maurer, F.; Koziczak, M.; Barbas, C. F., 3rd; Hynes, N. E. The ErbB2/ErbB3 heterodimer functions as an oncogenic unit: ErbB2 requires ErbB3 to drive breast tumor cell proliferation Proc. Natl. Acad. Sci. U. S. A. 2003, 100 (15) 8933-8
30. Eckstein, N.; Servan, K.; Girard, L.; Cai, D.; von Jonquieres, G.; Jaehde, U.; Kassack, M. U.; Gazdar, A. F.; Minna, J. D.; Royer, H. D. Epidermal growth factor receptor pathway analysis identifies amphiregulin as a key factor for cisplatin resistance of human breast cancer cells J. Biol. Chem. 2008, 283 (2) 739-50
31. Komurasaki, T.; Toyoda, H.; Uchida, D.; Morimoto, S. Epiregulin binds to epidermal growth factor receptor and ErbB-4 and induces tyrosine phosphorylation of epidermal growth factor receptor, ErbB-2, ErbB-3 and ErbB-4 Oncogene 1997, 15 (23) 2841-8
32. Futreal, P. A.; Coin, L.; Marshall, M.; Down, T.; Hubbard, T.; Wooster, R.; Rahman, N.; Stratton, M. R. A census of human cancer genes Nat. Rev. Cancer 2004, 4, 7
33. Downward, J. Targeting RAS signalling pathways in cancer therapy Nat. Rev. Cancer 2003, 3 (1) 12
34. Wu, C.; Zhu, J.; Zhang, X. Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes BMC Bioinf. 2012, 13, 182
35. Lessner, D. J.; Li, L.; Li, Q.; Rejtar, T.; Andreev, V. P.; Reichlen, M.; Hill, K.; Moran, J. J.; Karger, B. L.; Ferry, J. G. An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (47) 17921-6
36. Kauraniemi, P.; Barlund, M.; Monni, O.; Kallioniemi, A. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays Cancer Res. 2001, 61, 6
37. Lamorte, L.; Royal, I.; Naujokas, M.; Park, M. Crk adapter proteins promote an epithelial-mesenchymal-like transition and are required for HGF-mediated cell spreading and breakdown of epithelial adherens junctions Mol. Biol. Cell 2002, 13 (5) 1449-61
38. Padmanabhan, R. A.; Nirmala, L.; Murali, M.; Laloraya, M. CrkL is a co-activator of estrogen receptor α that enhances tumorigenic potential in cancer Mol. Endocrinol. 2011, 25 (9) 1499-512
39. Paredes, J.; Correia, A. L.; Ribeiro, A. S.; Milanezi, F.; Cameselle-Teijeiro, J.; Schmitt, F. C. Breast carcinomas that co-express E- and P-cadherin are associated with p120-catenin cytoplasmic localisation and poor patient survival J. Clin. Pathol. 2008, 61 (7) 856-62
40. Paredes, J.; Correia, A. L.; Ribeiro, A. S.; Schmitt, F. Expression of p120-catenin isoforms correlates with genomic and transcriptional phenotype of breast cancer cell lines Cell. Oncol. 2007, 29 (6) 467-76
41. Saijo, Y.; Perlaky, L.; Valdez, B. C.; Busch, R. K.; Henning, D.; Zhang, W. W.; Busch, H. The effect of antisense p120 construct on p120 expression and cell proliferation in human breast cancer MCF-7 cells Cancer Lett. 1993, 68 (2-3) 95-104
42. Pinilla, S. M.; Honrado, E.; Hardisson, D.; Benitez, J.; Palacios, J. Caveolin-1 expression is associated with a basal-like phenotype in sporadic and hereditary breast cancer Breast Cancer Res. Treat. 2006, 99 (1) 85-90
43. Agelaki, S.; Spiliotaki, M.; Markomanolaki, H.; Kallergi, G.; Mavroudis, D.; Georgoulias, V.; Stournaras, C. Caveolin-1 regulates EGFR signaling in MCF-7 breast cancer cells and enhances gefitinib-induced tumor cell inhibition Cancer Biol. Ther. 2009, 8 (15) 1470-7
44. Tan, D. S.; Marchio, C.; Jones, R. L.; Savage, K.; Smith, I. E.; Dowsett, M.; Reis-Filho, J. S. Triple negative breast cancer: molecular profiling and prognostic impact in adjuvant anthracycline-treated patients Breast Cancer Res. Treat. 2008, 111 (1) 27-44
45. Stein, D.; Wu, J.; Fuqua, S. A.; Roonprapunt, C.; Yajnik, V.; D'Eustachio, P.; Moskow, J. J.; Buchberg, A. M.; Osborne, C. K.; Margolis, B. The SH2 domain protein GRB-7 is co-amplified, overexpressed and in a tight complex with HER2 in breast cancer EMBO J. 1994, 13 (6) 1331-40
46. Ravid, D.; Chuderland, D.; Landsman, L.; Lavie, Y.; Reich, R.; Liscovitch, M. Filamin A is a novel caveolin-1-dependent target in IGF-I-stimulated cancer cell migration Exp. Cell Res. 2008, 314 (15) 2762-73
47. Tulchin, N.; Chambon, M.; Juan, G.; Dikman, S.; Strauchen, J.; Ornstein, L.; Billack, B.; Woods, N. T.; Monteiro, A. N. BRCA1 protein and nucleolin colocalize in breast carcinoma tissue and cancer cell lines Am. J. Pathol. 2010, 176 (3) 1203-14
48. Li, J.; Yang, L.; Song, L.; Xiong, H.; Wang, L.; Yan, X.; Yuan, J.; Wu, J.; Li, M. Astrocyte elevated gene-1 is a proliferation promoter in breast cancer via suppressing transcriptional factor FOXO1 Oncogene 2009, 28 (36) 3188-96
49. Li, J.; Zhang, N.; Song, L. B.; Liao, W. T.; Jiang, L. L.; Gong, L. Y.; Wu, J.; Yuan, J.; Zhang, H. Z.; Zeng, M. S.; Li, M. Astrocyte elevated gene-1 is a novel prognostic marker for breast cancer progression and overall patient survival Clin. Cancer Res. 2008, 14 (11) 3319-26
50. Marty, B.; Maire, V.; Gravier, E.; Rigaill, G.; Vincent-Salomon, A.; Kappler, M.; Lebigot, I.; Djelti, F.; Tourdès, A.; Gestraud, P. Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells Breast Cancer Res. 2008, 10 (6) R101
51. Cheol Kim, D.; Thorat, M. A.; Lee, M. R.; Cho, S. H.; Vasiljević, N.; Scibior-Bentkowska, D.; Wu, K.; Ahmad, A. S.; Duffy, S.; Cuzick, J. M. Quantitative DNA methylation and recurrence of breast cancer: A study of 30 candidate genes Cancer Biomarkers 2011, 11 (2) 75-88
52. McKiernan, E.; McDermott, E. W.; Evoy, D.; Crown, J.; Duffy, M. J. The role of S100 genes in breast cancer progression Tumor Biol. 2011, 32 (3) 441-50
53. Ferguson, A. T.; Evron, E.; Umbricht, C. B.; Pandita, T. K.; Chan, T. A.; Hermeking, H.; Marks, J. R.; Lambers, A. R.; Futreal, P. A.; Stampfer, M. R.; Sukumar, S. High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (11) 6049-54
54. Lodygin, D.; Hermeking, H. Epigenetic silencing of 14-3-3sigma in cancer Semin. Cancer Biol. 2006, 16 (3) 214-24
55. Levine, J. J.; Stimson-Crider, K. M.; Vertino, P. M. Effects of methylation on expression of TMS1/ASC in human breast cancer cells Oncogene 2003, 22 (22) 3475-88
56. Vaught, D.; Brantley-Sieders, D. M.; Chen, J. Eph receptors in breast cancer: roles in tumor promotion and tumor suppression Breast Cancer Res. 2008, 10 (6) 217
57. Larsen, A. B.; Pedersen, M. W.; Stockhausen, M. T.; Grandal, M. V.; van Deurs, B.; Poulsen, H. S. Activation of the EGFR gene target EphA2 inhibits epidermal growth factor-induced cancer cell motility Mol. Cancer Res. 2007, 5 (3) 283-93