Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues

European Journal of Cancer

Volumn 46, Issue 1, 2010, Pages 47-55

  Berg, Daniela ^a   Hipp, Susanne ^a   Malinowsky, Katharina ^a   Böllner, Claudia ^a   Becker, Karl Friedrich ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Epidermal growth factor receptor I (EGFR); Formalin fixed; HER2; Mitogen activated protein kinase (MAPK); Paraffin embedded tissue (FFPE); Personalised cancer therapy

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; FORMALDEHYDE; MITOGEN ACTIVATED PROTEIN KINASE; PARAFFIN; PROTEIN; PROTEOME; RNA;

ARTICLE; CANCER DIAGNOSIS; CANCER THERAPY; CANCER TISSUE; CARCINOGENESIS; DRUG TARGETING; EXTRACTION; HISTOPATHOLOGY; HUMAN; MOLECULAR PROFILING; PATIENT SELECTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; REVERSE PHASE PROTEIN ARRAY; SIGNAL TRANSDUCTION; TISSUE FIXATION; TREATMENT PLANNING; TREATMENT RESPONSE;

FORMALDEHYDE; GENE EXPRESSION PROFILING; HUMANS; NEOPLASM PROTEINS; NEOPLASMS; PARAFFIN EMBEDDING; PATIENT SELECTION; PROGNOSIS; PROTEIN ARRAY ANALYSIS; PROTEOMICS; SIGNAL TRANSDUCTION; TISSUE FIXATION; TUMOR MARKERS, BIOLOGICAL;

EID: 71049161234     PISSN: 09598049     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejca.2009.10.016     Document Type: Article

References (48)

1. Cowherd S.M., Espina V.A., Petricoin III E.F., and Liotta L.A. Proteomic analysis of human breast cancer tissue with laser-capture microdessection and reverse-phase protein microarray. Clin Breast Cancer 5 (2004) 385-392
2. Dhanasekaran D.N., and Johnson G.L. MAPKs: function, regulation, role in cancer and therapeutic targeting. Oncogene 26 (2007) 3097-3099
3. Raman M., Chen W., and Cobb M.H. Differential regulation and properties of MAPKs. Oncogene 26 (2007) 3100-3112
4. Dancey J., and Sausville E.A. Issues and progress with protein kinase inhibitors for cancer treatment. Nat Rev Drug Discov 2 (2003) 296-313
5. Hynes N.E., and Lane H.A. ERBB receptors and cancer: the complexity of targeted inhibitors. Nat Rev Cancer 5 (2005) 341-354
6. Piccart M., Lohrisch C., Di Leo A., and Larsimont D. The predictive value of HER2 in breast cancer. Oncology 61 Suppl 2 (2001) 73-82
7. Emens L.A. Trastuzumab: targeted therapy for the management of HER-2/neu-overexpressing metastatic breast cancer. Am J Ther 12 (2005) 243-253
8. Slamon D.J., Godolphin W., Jones L.A., et al. Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 244 (1989) 707-712
9. Slamon D.J., Clark G.M., Wong S.G., Levin W.J., Ullrich A., and McGuire W.L. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235 (1987) 177-182
10. Wulfkuhle J.D., Speer R., Pierobon M., et al. Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res 7 (2008) 1508-1517
11. Becker K.F., Metzger V., Hipp S., and Hofler H. Clinical proteomics: new trends for protein microarrays. Curr Med Chem 13 (2006) 1831-1837
12. Becker K.F., Schott C., Hipp S., et al. Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis. J Pathol 211 (2007) 370-378
13. Lim M.S., and Elenitoba-Johnson K.S. Proteomics in pathology research. Lab Invest 84 (2004) 1227-1244
14. Liotta L., and Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 1 (2000) 48-56
15. Nirmalan N.J., Harnden P., Selby P.J., and Banks R.E. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol Biosyst 4 (2008) 712-720
16. Kroll J., Becker K.F., Kuphal S., Hein R., Hofstadter F., and Bosserhoff A.K. Isolation of high quality protein samples from punches of formalin fixed and paraffin embedded tissue blocks. Histol Histopathol 23 (2008) 391-395
17. Paweletz C.P., Charboneau L., Bichsel V.E., et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20 (2001) 1981-1989
18. Chu W.S., Liang Q., Liu J., et al. A nondestructive molecule extraction method allowing morphological and molecular analyses using a single tissue section. Lab Invest 85 (2005) 1416-1428
19. Ikeda K., Monden T., Kanoh T., et al. Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J Histochem Cytochem 46 (1998) 397-403
20. Nirmalan N.J., Harnden P., Selby P.J., and Banks R.E. Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting. J Pathol 217 (2009) 497-506
21. Chung J.Y., Lee S.J., Kris Y., Braunschweig T., Traicoff J.L., and Hewitt S.M. A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2 (2008) 1539-1547
22. Shi S.R., Liu C., Balgley B.M., Lee C., and Taylor C.R. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J Histochem Cytochem 54 (2006) 739-743
23. Becker K.F., Mack H., Schott C., et al. Extraction of phosphorylated proteins from formalin-fixed cancer cells and tissues. TOPATJ 2 (2008) 44-52
24. Becker K.F., Schott C., Becker I., and Höfler H. Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains. Proteomics Clin Appl 2 (2008) 737-743
25. Addis M.F., Tanca A., Pagnozzi D., Crobu S., Fanciulli G., Cossu-Rocca P., and Uzzau S. Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics 9 (2009) 3815-3823
26. Crockett D.K., Lin Z., Vaughn C.P., Lim M.S., and Elenitoba-Johnson K.S. Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab Invest 85 (2005) 1405-1415
27. Hood B.L., Darfler M.M., Guiel T.G., et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics 4 (2005) 1741-1753
28. Palmer-Toy D.E., Krastins B., Sarracino D.A., Nadol Jr. J.B., and Merchant S.N. Efficient method for the proteomic analysis of fixed and embedded tissues. J Proteome Res 4 (2005) 2404-2411
29. Sage L. Proteomics gets out of a fix. J Proteome Res 4 (2005) 1903-1904
30. Wulfkuhle J.D., Edmiston K.H., Liotta L.A., and Petricoin III E.F. Technology insight: pharmacoproteomics for cancer-promises of patient-tailored medicine using protein microarrays. Nat Clin Pract Oncol 3 (2006) 256-268
31. Grubb R.L., Calvert V.S., Wulkuhle J.D., et al. Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics 3 (2003) 2142-2146
32. Liotta L.A., Espina V., Mehta A.I., et al. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 3 (2003) 317-325
33. Sheehan K.M., Calvert V.S., Kay E.W., et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol Cell Proteomics 4 (2005) 346-355
34. Espina V., Mehta A.I., Winters M.E., et al. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 3 (2003) 2091-2100
35. Wulfkuhle J., Espina V., Liotta L., and Petricoin E. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer 40 (2004) 2623-2632
36. Templin M.F., Stoll D., Schrenk M., Traub P.C., Vohringer C.F., and Joos T.O. Protein microarray technology. Trends Biotechnol 20 (2002) 160-166
37. Feinberg J.G. A 'microspot' test for antigens and antibodies. Nature 192 (1961) 985-986
38. Philp A.J., Campbell I.G., Leet C., et al. The phosphatidylinositol 3′-kinase p85alpha gene is an oncogene in human ovarian and colon tumors. Cancer Res 61 (2001) 7426-7429
39. Shayesteh L., Lu Y., Kuo W.L., et al. PIK3CA is implicated as an oncogene in ovarian cancer. Nat Genet 21 (1999) 99-102
40. Fang J.Y., and Richardson B.C. The MAPK signalling pathways and colorectal cancer. Lancet Oncol 6 (2005) 322-327
41. Lobke C., Laible M., Rappl C., et al. Contact spotting of protein microarrays coupled with spike-in of normalizer protein permits time-resolved analysis of ERBB receptor signaling. Proteomics 8 (2008) 1586-1594
42. Gulmann C., Sheehan K.M., Conroy R.M., et al. Quantitative cell signalling analysis reveals down-regulation of MAPK pathway activation in colorectal cancer. J Pathol 218 (2009) 514-519
43. Lu X., and Kang Y. Organotropism of breast cancer metastasis. J Mammary Gland Biol Neoplasia 12 (2007) 153-162
44. Chambers A.F., Groom A.C., and MacDonald I.C. Dissemination and growth of cancer cells in metastatic sites. Nat Rev Cancer 2 (2002) 563-572
45. Belluco C., Mammano E., Petricoin E., et al. Kinase substrate protein microarray analysis of human colon cancer and hepatic metastasis. Clin Chim Acta 357 (2005) 180-183
46. Kim J.H., Kim M.A., Lee H.S., and Kim W.H. Comparative analysis of protein expressions in primary and metastatic gastric carcinomas. Hum Pathol 40 (2009) 314-322
47. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530-6.
48. Handschuh G., Candidus S., Luber B., et al. Tumour-associated E-cadherin mutations alter cellular morphology, decrease cellular adhesion and increase cellular motility. Oncogene 30 (1999) 4301-4312