An optimized method of metabolite extraction from formalin-fixed paraffin-embedded tissue for GC/MS analysis

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Wojakowska, Anna ^a   Marczak, Łukasz ^b   Jelonek, Karol ^a   Polanski, Krzysztof ^c   Widlak, Piotr ^a   Pietrowska, Monika ^a  

^a INSTITUTE OF ONCOLOGY   (Poland)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ASPARTIC ACID; BENZOIC ACID; CITRIC ACID; FORMALDEHYDE; GALACTOSE; GLUCOSE; GLUTAMIC ACID; GLYCERIC ACID; GLYCEROL; GLYCINE; GLYCOLIC ACID; GLYOXYLIC ACID; INOSITOL; LACTIC ACID; LYSINE; MALIC ACID; ORNITHINE; PARAFFIN; PYROGLUTAMIC ACID; PYRUVIC ACID; RIBITOL; SERINE; TAGATOSE; THREONINE; TIMONACIC; TYROSINE; UNINDEXED DRUG; VALINE; XYLOSE; AMINO ACID; CARBOXYLIC ACID; FATTY ACID;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EXTRACTION; HISTOLOGY; INTERMETHOD COMPARISON; KIDNEY; MALE; MASS FRAGMENTOGRAPHY; METABOLITE; METABOLOME; METABOLOMICS; MOUSE; NONHUMAN; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; TISSUE FIXATION; ANIMAL; CHEMISTRY; METABOLISM; PROCEDURES;

AMINO ACIDS; ANIMALS; CARBOXYLIC ACIDS; FATTY ACIDS; FORMALDEHYDE; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; METABOLOME; MICE; PARAFFIN; PARAFFIN EMBEDDING; TISSUE FIXATION;

EID: 84944346103     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0136902     Document Type: Article

References (21)

1. Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol Biosyst. 2008;4:712-720. doi: 10.1039/b800098k PMID: 18563244
2. Reimel BA, Pan S, May DH, Shaffer SA, Goodlett DR, McIntosh MW, et al. Proteomics on fixed tissue specimensa review. Curr Proteomics. 2009;6:63-69. PMID: 19829741
3. Klopfleisch R, Weiss AT, Gruber AD. Excavation of a buried treasure-DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol Histopathol. 2011;26:797-810. PMID: 21472693
4. Fox CH, Johnson FB, Whiting J, Roller PP. Formaldehyde fixation. J Histochem Cytochem. 1985;33:845-853. PMID: 3894502
5. Tanca A, Pagnozzi D, Addis MF. Setting proteins free: Progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin Appl. 2012;6:7-21. doi: 10.1002/prca. 201100044 PMID: 22213597
6. Maes E, Broeckx V, Mertens I, Sagaert X, Prenen H, Landuyt B, et al. Analysis of the formalin-fixed paraffinembedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids. 2013;45:205-218. doi: 10.1007/s00726-013-1494-0 PMID: 23592010
7. Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, et al. Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics. 2014;14:441-451. doi: 10.1002/pmic.201300311 PMID: 24339433
8. Kelly AD, Breitkopf SB, Yuan M, Goldsmith J, Spentzos D, Asara JM. Metabolomic Profiling from Formalin-Fixed, Paraffin-Embedded Tumor Tissue Using Targeted LC/MS/MS: Application in Sarcoma. PLoS ONE. 2011;6:e25357. doi: 10.1371/journal.pone.0025357 PMID: 21984915
9. Richter S, Peitzsch M, Rapizzi E, Lenders JW, Qin N, De Cubas AA, et al. Krebs Cycle Metabolite Profiling for Identification and Stratification of Pheochromocytomas/Paragangliomas due to Succinate Dehydrogenase Deficiency. J Clin Endocrinol Metab. 2014;99:3903-3911. doi: 10.1210/jc.2014-2151 PMID: 25014000
10. Yuan M, Breitkopf SB, Yang X, Asara JM. A positive/negative ion-switching, targeted mass spectrometrybased metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc. 2012;7:872-881. doi: 10.1038/nprot.2012.024 PMID: 22498707
11. Sahm F, Capper D, Pusch S, Balss J, Koch A, Langhans CD, et al. Detection of 2-hydroxyglutarate in formalin-fixed paraffin-embedded glioma specimens by gas chromatography/mass spectrometry. Brain Pathol. 2012;22:26-31. doi: 10.1111/j.1750-3639.2011.00506.x PMID: 21631627
12. Ng ESM, Kangarloo SB, Konno M, Paterson A, Magliocco AM. Extraction of tamoxifen and its metabolites from formalin-fixed, paraffin-embedded tissues: an innovative quantitation method using liquid chromatography and tandem mass spectrometry. Cancer Chemother Pharmacol. 2014;73:475-484. doi: 10.1007/s00280-013-2346-z PMID: 24414550
13. Denkert C, Budczies J, Kind T, Weichert W, Tablack P, Sehouli J, et al. Mass Spectrometry-Based Metabolic Profiling Reveals Different Metabolite Patterns in Invasive Ovarian Carcinomas and Ovarian Borderline Tumors, Cancer Res. 2006;66:10795-10804. PMID: 17108116
14. Shi SR, Gu J, Turrens J. Antigen Retrieval Techniques: Immunohistochemistry and Molecular Morphology. Natick, MA, Eaton Publishing; 2000. pp. 17-40.
15. Ganti S, Taylor SL, Abu Aboud O, Yang J, Evans C, Osier MV, et al. Kidney tumor biomarkers revealed by simultaneous multiple matrix metabolomics analysis. Cancer Res. 2012;72:3471-3479. doi: 10. 1158/0008-5472. CAN-11-3105 PMID: 22628425
16. Hughes C, Gaunt L, Brown M, Clarke NW, Gardner P. Assessment of paraffin removal from prostate FFPE sections using transmission mode FTIR-FPA imaging. Anal Methods. 2014;6:1028-1035.
17. Atkins D, Reiffen KA, Tegtmeier CL, Winther H, Bonato MS, Störkel S. Immunohistochemical detection of EGFR in paraffin-embedded tumor tissues: variation in staining intensity due to choice of fixative and storage time of tissue sections. J Histochem Cytochem. 2004;52:893-901. PMID: 15208356
18. Khoury T, Sait S, Hwang H, Chandrasekhar R, Wilding G, Tan D, et al. Delay to formalin fixation effect on breast biomarkers. Mod Pathol. 2009;22:1457-67. doi: 10.1038/modpathol.2009.117 PMID: 19734848
19. Hackett MJ, McQuillan JA, El-Assaad F, Aitken JB, Levina A, Cohen DD, et al. Chemical alterations to murine brain tissue induced by formalin fixation: implications for biospectroscopic imaging and mapping studies of disease pathogenesis. Analyst. 2011;136:2941-52. doi: 10.1039/c0an00269k PMID: 21629894
20. Xu H, Yang L, Wang W, Shi SR, Liu C, Liu Y, et al. Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res. 2008;7:1098-1108. doi: 10.1021/pr7006768 PMID: 18257518
21. Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, 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. doi: 10.1074/mcp. M800518-MCP200 PMID: 19467989