Application of 2D-DIGE to formalin-fixed diseased tissue samples from hospital repositories: Results from four case studies

Proteomics - Clinical Applications

Volumn 7, Issue 3-4, 2013, Pages 252-263

  Tanca, Alessandro ^a   Pisanu, Salvatore ^a   Biosa, Grazia ^a   Pagnozzi, Daniela ^a   Antuofermo, Elisabetta ^b   Burrai, Giovanni P ^b   Canzonieri, Vincenzo ^c   Cossu Rocca, Paolo ^b   Re, Valli De ^c   Eccher, Albino ^d   Fanciulli, Giuseppe ^b   Rocca, Stefano ^b   Uzzau, Sergio ^a,b   Addis, Maria Filippa ^a  

^a Porto Conte Ricerche Srl   (Italy)

^b UNIVERSITY OF SASSARI   (Italy)

^c CENTRO DI RIFERIMENTO ONCOLOGICO   (Italy)

^d UNIVERSITY OF VERONA   (Italy)

Author keywords

Canine mammary tumor; FFPE; Gastric adenocarcinoma; Gel based proteomics; Lung neuroendocrine tumor

Indexed keywords

CYANINE DYE; FORMALDEHYDE; PROTEIN;

ANIMAL TISSUE; ARTICLE; BREAST CARCINOMA; BREAST TUBULOPAPILLARY CARCINOMA; CANCER TISSUE; CHEMICAL LABELING; CONTROLLED STUDY; DOG; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE; HEAVY METAL POISONING; HOSPITAL; HUMAN; HUMAN TISSUE; IMAGE ANALYSIS; IMAGE QUALITY; LIVER CLOUDY SWELLING DEGENERATION; LIVER DISEASE; LIVER PARENCHYMA; LUNG SMALL CELL CANCER; LUNG TUMOR; MASS SPECTROMETRY; NEUROENDOCRINE TUMOR; NONHUMAN; NUCLEOTIDE SEQUENCE; PATIENT INFORMATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; QUALITY CONTROL; SHEEP; STOMACH ADENOCARCINOMA; STOMACH MUCOSA; TISSUE FIXATION; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS;

ANIMALS; BIOLOGICAL MARKERS; DOGS; FORMALDEHYDE; HUMANS; LUNG NEOPLASMS; PARAFFIN EMBEDDING; PROTEINS; PROTEOMICS; SHEEP; SMALL CELL LUNG CARCINOMA; TISSUE BANKS; TISSUE FIXATION; TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS;

OVIS ARIES;

EID: 84876338400     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201200054     Document Type: Article

References (55)

1. Nirmalan, N. J., Harnden, P., Selby, P. J., Banks, R. E., Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol. Biosyst. 2008, 4, 712-720.
2. Blonder, J., Veenstra, T. D., Clinical proteomic applications of formalin-fixed paraffin-embedded tissues. Clin. Lab. Med. 2009, 29, 101-113.
3. Tanca, A., Pagnozzi, D., Addis, M. F., Setting proteins free: progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin. Appl. 2012, 6, 7-21.
4. Magdeldin, S., Yamamoto, T., Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012, 12, 1045-1058.
5. Ralton, L. D., Murray, G. I., The use of formalin fixed wax embedded tissue for proteomic analysis. J. Clin. Pathol. 2011, 64, 297-302.
6. Addis, M. F., Tanca, A., Pagnozzi, D., Rocca, S. et al., 2-D PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues. Proteomics 2009, 9, 4329-4339.
7. Azimzadeh, O., Barjaktarovic, Z., Aubele, M., Calzada-Wack, J. et al., Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J. Proteome Res. 2010, 9, 4710-4720.
8. Tanca, A., Pagnozzi, D., Falchi, G., Tonelli, R. et al., Application of 2-D DIGE to formalin-fixed, paraffin-embedded tissues. Proteomics 2011, 11, 1005-1011.
9. Shi, S., Key, M., Kalra, K., Antigen retrieval in formalin-fixed, paraffin-embedded tissues: an enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections. J. Histochem. Cytochem. 1991, 39, 741-748.
10. Shi, S. R., Shi, Y., Taylor, C. R., Antigen retrieval immunohistochemistry: review and future prospects in research and diagnosis over two decades. J. Histochem. Cytochem. 2011, 59, 13-32.
11. Celis, J. E., Gel-based proteomics: what does MCP expect? Mol. Cell. Proteomics 2004, 3, 949.
12. Chevalier, F., Highlights on the capacities of "Gel-based" proteomics. Proteome Sci. 2010, 8, 23.
13. Unlu, M., Morgan, M. E., Minden, J. S., Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18, 2071-2077.
14. Lilley, K. S., Friedman, D. B., All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1, 401-409.
15. Viswanathan, S., Unlu, M., Minden, J. S., Two-dimensional difference gel electrophoresis. Nat. Protoc. 2006, 1, 1351-1358.
16. Addis, M. F., Tanca, A., Pagnozzi, D., Crobu, S. et al., Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics 2009, 9, 3815-3823.
17. Pisanu, S., Ghisaura, S., Pagnozzi, D., Biosa, G. et al., The sheep milk fat globule membrane proteome. J. Proteomics 2011, 74, 350-358.
18. Biosa, G., Addis, M. F., Tanca, A., Pisanu, S. et al., Comparison of blood serum peptide enrichment methods by Tricine SDS-PAGE and mass spectrometry. J. Proteomics 2011, 75, 93-99.
19. Olsen, J. V., de Godoy, L. M., Li, G., Macek, B. et al., Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 2005, 4, 2010-2021.
20. Oien, K. A., McGregor, F., Butler, S., Ferrier, R. K. et al., Gastrokine 1 is abundantly and specifically expressed in superficial gastric epithelium, down-regulated in gastric carcinoma, and shows high evolutionary conservation. J. Pathol. 2004, 203, 789-797.
21. Taniguchi, S., Suppression of cancer phenotypes through a multifunctional actin-binding protein, calponin, that attacks cancer cells and simultaneously protects the host from invasion. Cancer Sci. 2005, 96, 738-746.
22. Tee, Y. T., Chen, G. D., Lin, L. Y., Ko, J. L. et al., Nm23-H1: a metastasis-associated gene. Taiwan J. Obstet. Gynecol. 2006, 45, 107-113.
23. Jeon, T. Y., Han, M. E., Lee, Y. W., Lee, Y. S. et al., Overexpression of stathmin1 in the diffuse type of gastric cancer and its roles in proliferation and migration of gastric cancer cells. Br. J. Cancer 2010, 102, 710-718.
24. Gong, Y. H., Chen, M., Xu, Y., Dong, N. et al., Subtractive hybridization analysis of gastric diseases-associated Helicobacter pylori identifies peptidyl-prolyl isomerase as a potential marker for gastric cancer. FEMS Microbiol. Lett. 2011, 320, 103-109.
25. Rekhtman, N., Neuroendocrine tumors of the lung: an update. Arch. Pathol. Lab. Med. 2010, 134, 1628-1638.
26. Fricker, L. D., McKinzie, A. A., Sun, J., Curran, E. et al., Identification and characterization of proSAAS, a granin-like neuroendocrine peptide precursor that inhibits prohormone processing. J. Neurosci. 2000, 20, 639-648.
27. Lee, H. S., Park, J. W., Chertov, O., Colantonio, S. et al., Matrix-assisted laser desorption/ionization mass spectrometry reveals decreased calcylcin expression in small cell lung cancer. Pathol. Int. 2012, 62, 28-35.
28. Sofiadis, A., Dinets, A., Orre, L. M., Branca, R. M. et al., Proteomic study of thyroid tumors reveals frequent up-regulation of the Ca2+ -binding protein S100A6 in papillary thyroid carcinoma. Thyroid 2010, 20, 1067-1076.
29. Koshimizu, H., Kim, T., Cawley, N. X., Loh, Y. P., Chromogranin A: a new proposal for trafficking, processing and induction of granule biogenesis. Regul. Pept. 2010, 160, 153-159.
30. Wardman, J. H., Berezniuk, I., Di, S., Tasker, J. G. et al., ProSAAS-derived peptides are colocalized with neuropeptide Y and function as neuropeptides in the regulation of food intake. PLoS ONE 2011, 6, e28152.
31. Klopfleisch, R., Klose, P., Weise, C., Bondzio, A. et al., Proteome of metastatic canine mammary carcinomas: similarities to and differences from human breast cancer. J. Proteome Res. 2010, 9, 6380-6391.
32. Rower, C., Ziems, B., Radtke, A., Schmitt, O. et al., Toponostics of invasive ductal breast carcinoma: combination of spatial protein expression imaging and quantitative proteome signature analysis. Int. J. Clin. Exp. Pathol. 2011, 4, 454-467.
33. Rower, C., Koy, C., Hecker, M., Reimer, T. et al., Mass spectrometric characterization of protein structure details refines the proteome signature for invasive ductal breast carcinoma. J. Am. Soc. Mass Spectrom. 2011, 22, 440-456.
34. Chang, X. Z., Li, D. Q., Hou, Y. F., Wu, J. et al., Identification of the functional role of peroxiredoxin 6 in the progression of breast cancer. Breast Cancer Res. 2007, 9, R76.
35. Goncalves, K., Sullivan, K., Phelan, S., Differential expression and function of peroxiredoxin 1 and peroxiredoxin 6 in cancerous MCF-7 and noncancerous MCF-10A breast epithelial cells. Cancer Invest. 2012, 30, 38-47.
36. Alanen, H. I., Williamson, R. A., Howard, M. J., Hatahet, F. S. et al., ERp27, a new non-catalytic endoplasmic reticulum-located human protein disulfide isomerase family member, interacts with ERp57. J. Biol. Chem. 2006, 281, 33727-33738.
37. Wong, L. L., Fan, S. T., Man, K., Sit, W. H. et al., Identification of liver proteins and their roles associated with carbon tetrachloride-induced hepatotoxicity. Hum. Exp. Toxicol. 2011, 30, 1369-1381.
38. Shinkai, Y., Yamamoto, C., Kaji, T., Lead induces the expression of endoplasmic reticulum chaperones GRP78 and GRP94 in vascular endothelial cells via the JNK-AP-1 pathway. Toxicol. Sci. 2010, 114, 378-386.
39. Lou, L. X., Geng, B., Chen, Y., Yu, F. et al., Endoplasmic reticulum stress involved in heart and liver injury in iron-loaded rats. Clin. Exp. Pharmacol. Physiol. 2009, 36, 612-618.
40. Liu, F., Inageda, K., Nishitai, G., Matsuoka, M., Cadmium induces the expression of Grp78, an endoplasmic reticulum molecular chaperone, in LLC-PK1 renal epithelial cells. Environ. Health Perspect. 2006, 114, 859-864.
41. Sprung, R. W., Brock, J. W. C., Tanksley, J. P., Li, M. et al., Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics 2009, 8, 1988-1998.
42. Wolff, C., Schott, C., Porschewski, P., Reischauer, B. et al., Successful protein extraction from over-fixed and long-term stored formalin-fixed tissues. PLoS ONE 2011, 6, e16353.
43. Tanca, A., Pagnozzi, D., Falchi, G., Biosa, G. et al., Impact of fixation time on GeLC-MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues. J. Proteomics 2011, 74, 1015-1021.
44. Nirmalan, N. J., Harnden, P., Selby, P. J., 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. 2009, 217, 497-506.
45. Rabek, J. P., Boylston, W. H., 3rd, Papaconstantinou, J., Carbonylation of ER chaperone proteins in aged mouse liver. Biochem. Biophys. Res. Commun. 2003, 305, 566-572.
46. Song, J., Finnerty, C. C., Herndon, D. N., Boehning, D. et al., Severe burn-induced endoplasmic reticulum stress and hepatic damage in mice. Mol. Med. 2009, 15, 316-320.
47. Alanen, H. I., Williamson, R. A., Howard, M. J., Hatahet, F. S. et al., ERp27, a new non-catalytic endoplasmic reticulum-located human protein disulfide isomerase family member, interacts with ERp57. J. Biol. Chem. 2006, 281, 33727-33738.
48. Liu, F., Inageda, K., Nishitai, G., Matsuoka, M., Cadmium induces the expression of Grp78, an endoplasmic reticulum molecular chaperone, in LLC-PK1 renal epithelial cells. Environ. Health Perspect. 2006, 114, 859-864.
49. Lou, L. X., Geng, B., Chen, Y., Yu, F. et al., Endoplasmic reticulum stress involved in heart and liver injury in iron-loaded rats. Clin. Exp. Pharmacol. Physiol. 2009, 36, 612-618.
50. Qian, Y., Zheng, Y., Ramos, K. S., Tiffany-Castiglioni, E., GRP78 compartmentalized redistribution in Pb-treated glia: role of GRP78 in lead-induced oxidative stress. Neurotoxicology 2005, 26, 267-275.
51. Morrison, D. K., The 14-3-3 proteins: integrators of diverse signalling cues that impact cell fate and cancer development. Trends Cell. Biol. 2009, 19, 16-23.
52. Lee, I. N., Chen, C. H., Sheu, J. C., Lee, H. S. et al., Identification of human hepatocellular carcinoma-related biomarkers by two-dimensional difference gel electrophoresis and mass spectrometry. J. Proteome Res. 2005, 4, 2062-2069.
53. Grune, T., Reinheckel, T., Li, R., North, J. A. et al., Proteasome-dependent turnover of protein disulfide isomerase in oxidatively stressed cells. Arch. Biochem. Biophys. 2002, 397, 407-413.
54. Wu, W. W., Wang, G., Baek, S. J., Shen R. F., Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D Gel- or LC-MALDI TOF/TOF. J. Proteome Res. 2006, 5, 651-658.
55. Piersma, S. R., Fiedler, U., Span, S., Lingnau, A. et al., Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. J. Proteome Res. 2010, 9, 1913-1922.