Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue

Proteomics - Clinical Applications

Volumn 7, Issue 3-4, 2013, Pages 241-251

  Thompson, Seonaid M ^a   Craven, Rachel A ^a   Nirmalan, Niroshini J ^b   Harnden, Patricia ^c   Selby, Peter J ^a   Banks, Rosamonde E ^a  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

^b UNIVERSITY OF SALFORD   (United Kingdom)

^c LEEDS TEACHING HOSPITALS NHS TRUST   (United Kingdom)

Author keywords

Biomarkers; Formalin fixed paraffin embedded; Pre analytical; Tissue

Indexed keywords

BIOLOGICAL MARKER; FORMALDEHYDE;

ANALYTICAL PARAMETERS; BREAST CANCER; CANCER TISSUE; COLD ISCHEMIA; FIXATION DURATION; FIXATION TEMPERATURE; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE; FROZEN SECTION; HISTOPATHOLOGY; HUMAN; IMMUNOHISTOCHEMISTRY; ISCHEMIA; KIDNEY CARCINOMA; LIQUID CHROMATOGRAPHY; PHYSICAL PARAMETERS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEIN STABILITY; PROTEOMICS; REVIEW; SAMPLE SIZE; STORAGE; STORAGE TIME; TANDEM MASS SPECTROMETRY; TISSUE FIXATION; TISSUE MICROARRAY; TISSUE PROCESSING; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BIOLOGICAL MARKERS; FIXATIVES; FORMALDEHYDE; HUMANS; PARAFFIN; PARAFFIN EMBEDDING; PROTEINS; PROTEOME; PROTEOMICS; TISSUE FIXATION;

EID: 84876316245     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201200086     Document Type: Review

References (59)

1. Fox, C. H., Johnson, F. B., Whiting, J., Roller, P. P., Formaldehyde fixation. J. Histochem. Cytochem. 1985, 33, 845-853.
2. Ralton, L. D., Murray, G. I., The use of formalin fixed wax embedded tissue for proteomic analysis. J. Clin. Pathol. 2011, 64, 297-302.
3. Magdeldin, S., Yamamoto, T., Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012, 12, 1045-1058.
4. 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.
5. Hood, B. L., Darfler, M. M., Guiel, T. G., Furusato, B. et al., Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell Proteomics 2005, 4, 1741-1753.
6. Sprung Jr, R. W., Brock, J. W., 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.
7. Guzel, C., Ursem, N. T., Dekker, L. J., Derkx, P. et al., Multiple reaction monitoring assay for pre-eclampsia related calcyclin peptides in formalin fixed paraffin embedded placenta. J. Proteome Res. 2011, 10, 3274-3282.
8. Wisniewski, J. R., Ostasiewicz, P., Mann, M., High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome Res. 2011, 10, 3040-3049.
9. Negishi, A., Masuda, M., Ono, M., Honda, K. et al., Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Cancer Sci. 2009, 100, 1605-1611.
10. Patel, V. J., Thalassinos, K., Slade, S. E., Connolly, J. B. et al., A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J. Proteome Res. 2009, 8, 3752-3759.
11. Byrum, S., Avaritt, N. L., Mackintosh, S. G., Munkberg, J. M. et al., A quantitative proteomic analysis of FFPE melanoma. J. Cutan. Pathol. 2011, 38, 933-936.
12. Nomura, H., Sakai, A., Nagano, M., Umino, M. et al., Expression changes of cation chloride cotransporters in the rat spinal cord following intraplantar formalin. Neurosci. Res. 2006, 56, 435-440.
13. 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.
14. Naidoo, K., Jones, R., Dmitrovic, B., Wijesuriya, N. et al., Proteome of formalin-fixed paraffin-embedded pancreatic ductal adenocarcinoma and lymph node metastases. J. Pathol. 2012, 226, 756-763.
15. Jain, M. R., Liu, T., Hu, J., Darfler, M. et al., Quantitative proteomic analysis of formalin fixed paraffin embedded oral HPV lesions from HIV patients. Open Proteomics J. 2008, 1, 40-45.
16. Xiao, B., Liu, Z., Li, B. S., Tang, B. et al., Induction of microRNA-155 during Helicobacter pylori infection and its negative regulatory role in the inflammatory response. J. Infect. Dis. 2009, 200, 916-925.
17. Ostasiewicz, P., Zielinska, D. F., Mann, M., Wisniewski, J. R., Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 2010, 9, 3688-3700.
18. Nishimura, T., Nomura, M., Tojo, H., Hamasaki, H. et al., Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon non-metastatic lung adenocarcinoma. J. Proteomics 2010, 73, 1100-1110.
19. Kawamura, T., Nomura, M., Tojo, H., Fujii, K. et al., Proteomic analysis of laser-microdissected paraffin-embedded tissues: (1) stage-related protein candidates upon non-metastatic lung adenocarcinoma. J. Proteomics 2010, 73, 1089-1099.
20. Ikeda, K., Monden, T., Kanoh, T., Tsujie, M. et al., Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J. Histochem. Cytochem. 1998, 46, 397-403.
21. 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.
22. Chung, J. Y., Lee, S. J., Kris, Y., Braunschweig, T. et al., A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin. Appl. 2008, 2, 1539-1547.
23. Berg, D., Wolff, C., Langer, R., Schuster, T. et al., Discovery of new molecular subtypes in oesophageal adenocarcinoma. PLoS One 2011, 6, e23985.
24. Babic, A., Loftin, I. R., Stanislaw, S., Wang, M. et al., The impact of pre-analytical processing on staining quality for H&E, dual hapten, dual color in situ hybridization and fluorescent in situ hybridization assays. Methods 2010, 52, 287-300.
25. Pierceall, W. E., Wolfe, M., Suschak, J., Chang, H. et al., Strategies for H-score normalization of preanalytical technical variables with potential utility to immunohistochemical-based biomarker quantitation in therapeutic response diagnostics. Anal. Cell Pathol. (Amst.) 2011, 34, 159-168.
26. Engel, K. B., Moore, H. M., Effects of preanalytical variables on the detection of proteins by immunohistochemistry in formalin-fixed, paraffin-embedded tissue. Arch. Pathol. Lab. Med. 2011, 135, 537-543.
27. Espina, V., Mueller, C., Reduction of preanalytical variability in specimen procurement for molecular profiling. Methods Mol. Biol. 2012, 823, 49-57.
28. Hicks, D. G., Boyce, B. F., The challenge and importance of standardizing pre-analytical variables in surgical pathology specimens for clinical care and translational research. Biotech. Histochem. 2012, 87, 14-17.
29. Hewitt, S. M., Lewis, F. A., Cao, Y., Conrad, R. C. et al., Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Arch. Pathol. Lab. Med. 2008, 132, 1929-1935.
30. Espina, V., Edmiston, K. H., Heiby, M., Pierobon, M. et al., A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol. Cell Proteomics 2008, 7, 1998-2018.
31. Espina, V., Mueller, C., Edmiston, K., Sciro, M. et al., Tissue is alive: new technologies are needed to address the problems of protein biomarker pre-analytical variability. Proteomics Clin. Appl. 2009, 3, 874-882.
32. Li, J., Gould, T. D., Yuan, P., Manji, H. K. et al., Post-mortem interval effects on the phosphorylation of signaling proteins. Neuropsychopharmacology 2003, 28, 1017-1025.
33. Li, X., Friedman, A. B., Roh, M. S., Jope, R. S., Anesthesia and post-mortem interval profoundly influence the regulatory serine phosphorylation of glycogen synthase kinase-3 in mouse brain. J. Neurochem. 2005, 92, 701-704.
34. Sarto, C., Valsecchi, C., Mocarelli, P., Renal cell carcinoma: handling and treatment. Proteomics 2002, 2, 1627-1629.
35. Spruessel, A., Steimann, G., Jung, M., Lee, S. A. et al., Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques 2004, 36, 1030-1037.
36. Jackson, D., Rowlinson, R. A., Eaton, C. K., Nickson, J. A. et al., Prostatic tissue protein alterations due to delayed time to freezing. Proteomics 2006, 6, 3901-3908.
37. Skold, K., Svensson, M., Norrman, M., Sjogren, B. et al., The significance of biochemical and molecular sample integrity in brain proteomics and peptidomics: stathmin 2-20 and peptides as sample quality indicators. Proteomics 2007, 7, 4445-4456.
38. Ferrer, I., Santpere, G., Arzberger, T., Bell, J. et al., Brain protein preservation largely depends on the postmortem storage temperature: implications for study of proteins in human neurologic diseases and management of brain banks: a BrainNet Europe Study. J. Neuropathol. Exp. Neurol. 2007, 66, 35-46.
39. Crecelius, A., Gotz, A., Arzberger, T., Frohlich, T. et al., Assessing quantitative post-mortem changes in the gray matter of the human frontal cortex proteome by 2-D DIGE. Proteomics 2008, 8, 1276-1291.
40. Mueller, C., Edmiston, K. H., Carpenter, C., Gaffney, E. et al., One-step preservation of phosphoproteins and tissue morphology at room temperature for diagnostic and research specimens. PLoS One 2011, 6, e23780.
41. Espina, V., Mueller, C., Liotta, L. A., Phosphoprotein stability in clinical tissue and its relevance for reverse phase protein microarray technology. Methods Mol. Biol. 2011, 785, 23-43.
42. Pinhel, I. F., Macneill, F. A., Hills, M. J., Salter, J. et al., Extreme loss of immunoreactive p-Akt and p-Erk1/2 during routine fixation of primary breast cancer. Breast Cancer Res. 2010, 12, R76.
43. Chesnick, I. E., Mason, J. T., O'Leary, T. J., Fowler, C. B., Elevated pressure improves the rate of formalin penetration while preserving tissue morphology. J. Cancer 2010, 1, 178-183.
44. Puchtler, H., Meloan, S. N., On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. Histochemistry 1985, 82, 201-204.
45. Battifora, H., Effect of fixatives and fixation times on tissues. Am. J. Clin. Pathol. 1991, 96, 144-145.
46. Shi, S. R., Cote, R. J., Taylor, C. R., Antigen retrieval immunohistochemistry and molecular morphology in the year 2001. Appl. Immunohistochem. Mol. Morphol. 2001, 9, 107-116.
47. Xu, H., Yang, L., Wang, W., Shi, S. R. et al., Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J. Proteome Res. 2008, 7, 1098-1108.
48. 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.
49. Williams, J. H., Mepham, B. L., Wright, D. H., Tissue preparation for immunocytochemistry. J. Clin. Pathol. 1997, 50, 422-428.
50. Leong, T. Y., Cooper, K., Leong, A. S., Immunohistology-past, present, and future. Adv. Anat. Pathol. 2010, 17, 404-418.
51. Pollard, K., Lunny, D., Holgate, C. S., Jackson, P. et al., Fixation, processing, and immunochemical reagent effects on preservation of T-lymphocyte surface membrane antigens in paraffin-embedded tissue. J. Histochem. Cytochem. 1987, 35, 1329-1338.
52. Xie, R., Chung, J. Y., Ylaya, K., Williams, R. L. et al., Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections. J. Histochem. Cytochem. 2011, 59, 356-365.
53. Crockett, D. K., Lin, Z., Vaughn, C. P., Lim, M. S., Elenitoba-Johnson, K. S., Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab. Invest. 2005, 85, 1405-1415.
54. Hood, B. L., Conrads, T. P., Veenstra, T. D., Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics 2006, 6, 4106-4114.
55. Balgley, B. M., Guo, T., Zhao, K., Fang, X. et al., Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J. Proteome Res. 2009, 8, 917-925.
56. Jain, M. R., Li, Q., Liu, T., Rinaggio, J. et al., Proteomic identification of immunoproteasome accumulation in formalin-fixed rodent spinal cords with experimental autoimmune encephalomyelitis. J. Proteome Res. 2012, 11, 1791-1803.
57. Craven, R. A., Cairns, D. A., Zougman, A., Harnden, P. et al., Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age. Proteomics Clin. Appl. 2013, 7, 273-282
58. Signoretti, S., Bratslavsky, G., Waldman, F. M., Reuter, V. E. et al., Tissue-based research in kidney cancer: current challenges and future directions. Clin. Cancer Res. 2008, 14, 3699-3705.
59. von Wasielewski, R., Mengel, M., Wiese, B., Rudiger, T. et al., Tissue array technology for testing interlaboratory and interobserver reproducibility of immunohistochemical estrogen receptor analysis in a large multicenter trial. Am. J. Clin. Pathol. 2002, 118, 675-682.