Novel protein extraction approach using micro-sized chamber for evaluation of proteins eluted from formalin-fixed paraffin-embedded tissue sections

Proteome Science

Isamu Hayashi²  Tohru Mochizuki³  Taka-Aki Sato⁵  Takashi Nakajima²  Ken Yamaguchi¹  Shun-ichiro Ogura⁴  Yutaka Aoki⁵  Kanako Wakabayashi-Nakao³  Keiichi Hatakeyama³ 

[1] Shizuoka Cancer Center Hospital and Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan;Pathology Division, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan;Medical Genetics Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan;Frontier Research Center, Tokyo Institute of Technology, 4259-B102 Nagatsuta-cho, Midori-ku, Yokohama 226-8051, Japan;Life Science Research Center, Shimadzu Corporation, 1 Nishinokyo-Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan

关键词: Micro-sized chamber;    Mass spectrometry;    Heat-induced antigen retrieval;    Gastric cancer;    FFPE tissue;    Colon cancer;    Colon adenoma;    Antigen retrieval;   

Others  :  817477
DOI  :  10.1186/1477-5956-10-19

 received in 2012-02-16, accepted in 2012-03-23,  发布年份 2012

【 摘 要 】

We describe a novel antigen-retrieval method using a micro-sized chamber for mass spectrometry (MS) analysis to identify proteins that are preferentially eluted from formalin-fixed paraffin-embedded (FFPE) samples. This approach revealed that heat-induced antigen retrieval (HIAR) from an FFPE sample fixed on a glass slide not only improves protein identification, but also facilitates preferential elution of protein subsets corresponding to the properties of antigen-retrieval buffers. Our approach may contribute to an understanding of the mechanism of HIAR.

【 授权许可】

   
2012 Hatakeyama et al; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Conrads TP, Veenstra TD, Krizman DB: Liquid Tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 2005, 38:S32-S35.
• [2]Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB Jr, Merchant SN: Efficient method for the proteomic analysis of fixed and embedded tissues. J Proteome Res 2005, 4:2404-2411.
• [3]Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KS: Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab Invest 2005, 85:1405-1415.
• [4]Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, Sesterhenn IA, Conrads TP, Veenstra TD, Krizman DB: Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics 2005, 4:1741-1753.
• [5]Jiang X, Feng S, Tian R, Ye M, Zou H: Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J Proteome Res 2007, 6:1038-1047.
• [6]Ronci M, Bonanno E, Colantoni A, Pieroni L, Di Ilio C, Spagnoli LG, Federici G, Urbani A: Protein unlocking procedures of formalin-fixed paraffin-embedded tissues: application to MALDI-TOF imaging MS investigations. Proteomics 2008, 8:3702-3714.
• [7]Xu H, Yang L, Wang W, Shi SR, Liu C, Liu Y, Fang X, Taylor CR, Lee CS, Balgley BM: Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 2008, 7:1098-1108.
• [8]Groseclose MR, Massion PP, Chaurand P, Caprioli RM: High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 2008, 8:3715-3724.
• [9]Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC: 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.
• [10]Djidja MC, Claude E, Snel MF, Scriven P, Francese S, Carolan V, Clench MR: MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78 kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. J Proteome Res 2009, 8:4876-4884.
• [11]Azimzadeh O, Barjaktarovic Z, Aubele M, Calzada-Wack J, Sarioglu H, Atkinson MJ, Tapio S: Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J Proteome Res 2010, 9:4710-4720.
• [12]Nirmalan NJ, Hughes C, Peng J, McKenna T, Langridge J, Cairns DA, Harnden P, Selby PJ, Banks RE: Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. J Proteome Res 2011, 10:896-906.
• [13]Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, Weil RJ, DeVoe DL, Lee CS, Balgley BM: Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 2007, 55:763-772.
• [14]Scicchitano MS, Dalmas DA, Boyce RW, Thomas HC, Frazier KS: Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry. J Histochem Cytochem 2009, 57:849-860.
• [15]Addis MF, Tanca A, Pagnozzi D, Crobu S, Fanciulli G, Cossu-Rocca P, Uzzau S: Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics 2009, 9:3815-3823.
• [16]Shi SR, Key ME, Kalra KL: 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.
• [17]Shi SR, Chaiwun B, Young L, Cote RJ, Taylor CR: Antigen retrieval technique utilizing citrate buffer or urea solution for immunohistochemical demonstration of androgen receptor in formalin-fixed paraffin sections. J Histochem Cytochem 1993, 41:1599-1604.
• [18]Emoto K, Yamashita S, Okada Y: Mechanisms of heat-induced antigen retrieval: does pH or ionic strength of the solution play a role for refolding antigens? J Histochem Cytochem 2005, 53:1311-1321.
• [19]Wisztorski M, Franck J, Salzet M, Fournier I: MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample? Methods Mol Biol 2010, 656:303-322.
• [20]Gustafsson JO, Oehler MK, McColl SR, Hoffmann P: Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffin-embedded tissue. J Proteome Res 2010, 9:4315-4328.
• [21]Chu WS, Liang Q, Liu J, Wei MQ, Winters M, Liotta L, Sandberg G, Gong M: A nondestructive molecule extraction method allowing morphological and molecular analyses using a single tissue section. Lab Invest 2005, 85:1416-1428.
• [22]Ogura SI, Kaneko K, Miyajima S, Ohshima K, Yamaguchi K, Mochizuki T: Proneurotensin/neuromedin N secreted from small cell lung carcinoma cell lines as a potential tumor marker. Proteom Clin Appl 2008, 2:1620-1627.
• [23]Hatakeyama K, Ohshima K, Fukuda Y, Ogura SI, Terashima M, Yamaguchi K, Mochizuki T: Identification of a novel protein isoform derived from cancer-related splicing variants using combined analysis of transcriptome and proteome. Proteomics 2011, 11:2275-2282.
• [24]Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M: Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
• [25]Shinoda K, Tomita M, Ishihama Y: emPAI Calc-for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics 2010, 26:576-577.
• [26]Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
• [27]Sipos T, Merkel JR: An effect of calcium ions on the activity, heat stability, and structure of trypsin. Biochemistry 1970, 9:2766-2775.
• [28]Katayama H, Nagasu T, Oda Y: Improvement of in-gel digestion protocol for peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2001, 15:1416-1421.
• [29]Wang N, Xu M, Wang P, Li L: Development of mass spectrometry-based shotgun method for proteome analysis of 500 to 5000 cancer cells. Anal Chem 2010, 82:2262-2271.
• [30]Yamashita S: Heat-induced antigen retrieval: mechanisms and application to histochemistry. Prog Histochem Cytochem 2007, 41:141-200.
• [31]Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305:567-580.
• [32]Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame AL, Unwin RJ: Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics 2005, 5:101-112.
• [33]Masuda T, Tomita M, Ishihama Y: Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 2008, 7:731-740.
• [34]Fowler CB, Cunningham RE, O'Leary TJ, Mason JT: 'Tissue surrogates' as a model for archival formalin-fixed paraffin-embedded tissues. Lab Invest 2007, 87:836-846.
• [35]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.
• [36]Metz B, Kersten GF, Hoogerhout P, Brugghe HF, Timmermans HA, de Jong A, Meiring H, ten Hove J, Hennink WE, Crommelin DJ, Jiskoot W: Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem 2004, 279:6235-6243.
• [37]Metz B, Kersten GFA, Baart GJE, de Jong A, Meiring H, ten Hove J, van Steenbergen M, Hennink W, Crommelin DJA, Jiskoot W: Identification of formaldehyde-induced modifications in proteins: reactions with insulin. Bioconjug Chem 2006, 17:815-822.