Separation and identification progress in cancer comparative proteomics

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1 Chinese Bulletin of Life Sciences Vol. 19, No. 1 Feb., (2007) Q51; R73 A Separation and identification progress in cancer comparative proteomics LI Xuanwen, CHEN Ping, ZHANG Lijun, LIANG Songping* (The Laboratory of Protein Chemistry and Proteomics, College of Life Sciences, Hunan Normal University, Changsha , China) Abstract: With the human genome sequence now determined, the field of cancer research is moving beyond genomics to proteomics. The comparative strategies involving in the cancer proteomic research have been developed, including cancer sample preparation, proteins or peptides separation, protein identification, bioinformatics, protein quantification and so on. All these will accelerate the identification of cancer markers that could be important in early detection, diagnosis and monitoring efficacy of treatment, and also the development of protein-based, cancer-specific targets, which have a great effect on cancer medicine. In this review, we focused on the sample separation and identification progress in cancer comparative proteomics. Key words: cancer; comparative proteomics; two-dimensional electrophoresis; liquid chromatography; quantification proteomics [1-2] DNA RNA Medline (2001 CB5120) (1980 ) (1946 ) * liangsp@hunnu.edu.cn

2 % 0.17% Medline 16% [3] (two dimensional electrophoresis, 2DE) (isoform) [4] [5] 3 MALDI-TOF ESI-Q- TOF PCR Sypro Ruby 2DE 2DE (fluorescence two-dimensional differential gel electrophoresis, DIGE) (Cy2 Cy3 Cy5) 50 µg 3, [6-7] 8 mol/l urea, 2 mol/l Thiourea, 65 mmol/l DTT, 0.5% Pharmalytes ph 3 10, 0.5 mmol/l PMSF, 4 % w/v CHAPS, 1% NP-40 / (4 1) 0.1 mol/l [8] 1.2 (liquid isoelectric focusing) (chromatofocusing) (non-porous silica reverse-phase high-performance liquid chromatography, NPS-RP-

3 99 HPLC) (electrospray ionization time-of-flight mass spectrometry, ESI-TOF- MS) (matrix-assisted laser desorption/ionization time of flight mass spectrometry, MALDI-TOF MS) Lubman MALDI-TOF-MS [9] 22 [10] Yates (shotgun) MudPIT (multidi-mensional protein identification technology) [11] bottom-up FT-MS top-down [12] (biomarker) (surface-enhanced laser desorption/ionization time of flight mass spectrometry, SELDI-TOF-MS) MALDI-TOF MS ( ) [13] MALDI-TOF (imaging mass spectromety) MALDI [14-15] 2.2

4 100 ( Sypro Ruby) ( DIGE) ( ) [16] (score) (unique peptides) (coverage) PAI (protein abundance index) (spectrum count) (extracted ion current, XIC) Andersen [17] empai (exponentially modified PAI) [18] LCMS [19] [16] (in vivo labeling) (in vitro labeling) Oda [20] ( 15 N 14 N ) 2DE MS (MS/MS) Ong Mann [16] SILAC (stable isotope labeling by amino acids in cell culture) Gronborg [21] SILAC [21] Krijgsveld [22] ( ) Ishihama [23] (culture-derived isotope tags, CDIT) N C Gygi [24] Cys ICAT (isotope-coded affinity tags) Cys ICAT ICAT ICAT [25] (cleavable ICAT, cicat) Sebastiano [26] Cys ICAI [16,27] Stewart [28] (cisplatin) ICAT 121 ICAT 500 (<7 )

5 101 Cys Lys Trp [29-30] ICAT ICAT ICAT Cys N Lys NIT (N-terminal isotope-encoded tagging) [31] 4 itraq (isobaric tags for relative and absolute quantitation) [32] MS/MS Keshamouni [33] itraq TGF-β - 51 Gerber [34] absolute quantification (AQUA) C C [35] ; (enzymatic labeling) 18 O 16 O C Zang [36] LCM 16 O/ 18 O [37] (de novo sequencing) icat itraq ABI (Applied Biosystem) ProQuant ProteinProspector Matthias Mann MSquant (differentially expressed protein database, DEPD) [38] ( hunnu.edu.cn:8080/depd/index.jsp)

6 102 [39-40] [41] [1] Sommer A, Haendler B. Androgen receptor and prostate cancer: molecular aspects and gene expression profiling. Curr Opin Drug Discov Devel, 2003, 6(5): [2] Simon R. Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data. Br J Cancer, 2003, 89(9): [3] Kolch W, Mischak H, Pitt A R. The molecular make-up of a tumour: proteomics in cancer research. Clin Sci (Lond), 2005, 108(5): [4] Hanash S M. Biomedical applications of two-dimensional electrophoresis using immobilized ph gradients: current status. Electrophoresis, 2000, 21(6): [5) Zhang L J, Liu X, Zhang J A, et al. Proteome analysis of combined effects of androgen and estrogen on the mouse mammary gland. Proteomics, 2006, 6(2): [6) Babu G J, Wheeler D, Alzate O, et al. Solubilization of membrane proteins for two-dimensional gel electrophoresis: identification of sarcoplasmic reticulum membrane proteins. Anal Biochem, 2004, 325(1): [7] Luche S, Santoni V, Rabilloud T. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics, 2003, 3(3): [8] Zhang L J, Xie J Y, Wang X E, et al. Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins. Proteomics, 2005, 5(17): [9] Wall D B, Kachman M T, Gong SY, et al. Isoelectric focusing nonporous RP HPLC: a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDI-TOF mass spectrometry. Anal Chem, 2000, 72(6): [10] Hamler R L, Zhu K, Buchanan N S, et al. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics, 2004, 4(3): [11] Steen H, Mann M. The ABC s (and XYZ s) of peptide sequencing. Nat Rev Mol Cell Biol, 2004, 5(9): [12] Yan F, He M, Hogan J M, et al. Targeted biomarker detection via whole protein ion trap tandem mass spectrometry: thymosin β4 in a human lung cancer cell line. J Mass Spectrom, 2005, 40(4): [13] Hu Y, Zhang S, Yu J, et al. SELDI-TOF-MS: the proteomics and bioinformatics approaches in the diagnosis of breast cancer. Breast, 2005, 14(4): [14] Schwartz S A, Weil R J, Johnson M D, et al. Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clin Cancer Res, 2004, 10(3): [15] Yanagisawa K, Shyr Y, Xu B J, et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet, 2003, 362(9382): [16] Ong S E, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol, 2005, 1(5): [17] Andersen J S, Wilkinson C J, Mayor T, et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature, 2003, 426(6966): [18] Ishihama Y, Oda Y, Tabata T, et al. 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(9): [19] Silva J C, Gorenstein M V, Li G Z, et al. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics, 2006, 5(1): [20] Oda Y, Huang K, Cross F R, et al. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA, 1999, 96(12): [21] Gronborg M, Kristiansen T Z, Iwahori A, et al. Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics, 2006, 5 (1): [22] Krijgsveld J, Ketting R F, Mahmoudi T, et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol, 2003, 21(8): [23] Ishihama Y, Sato T, Tabata T, et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat Biotechnol, 2005, 23(5): [24] Gygi S P, Rist B, Gerber S A, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 1999, 17(10): [25] Qiu Y, Sousa E A, Hewick R M, et al. Acid-labile isotopecoded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal Chem, 2002, 74(19): [26] Sebastiano R, Citterio A, Lapadula M, et al. A new deuterated alkylating agent for quantitative proteomics. Rapid Commun Mass Spectrom, 2003, 17(21): [27] Kuruma H, Egawa S, Oh-Ishi M, et al. Proteome analysis of prostate cancer. Prostate Cancer Prostatic Dis, 2005, 8(1): [28] Stewart J J, White J T, Yan X, et al. Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quan-

7 103 titative proteomic technology and integrated with mrna expression levels. Mol Cell Proteomics, 2006, 5(3): [29] Kuyama H, Watanabe M, Toda C, et al. An approach to quantitative proteome analysis by labeling tryptophan residues. Rapid Commun Mass Spectrom, 2003, 17(14): [30] Chakraborty A, Regnier F E. Global internal standard technology for comparative proteomics. J Chromatogr A, 2002, 949(1-2): [31] Zhang X, Jin Q K, Carr S A, et al. N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry. Rapid Commun Mass Spectrom, 2002, 16(24): [32] Ross P L, Huang Y N, Marchese J N, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents. Mol Cell Proteomics, 2004, 3(12): [33] Keshamouni V G, Michailidis G, Grasso C S, et al. Differential protein expression profiling by itraq-2dlc-ms/ms of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res, 2006, 5(5): [34] Gerber S A, Rush J, Stemman O, et al. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA, 2003, 100(12): [35] Goodlett D R, Keller A, Watts J D, et al. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom, 2001, 15(14): [36] Zang L, Palmer-Toy D, Hancock W S, et al. Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16 O/ 18 O isotopic labeling. J Proteome Res, 2004, 3(3): [37] Chalkley R J, Hansen K C, Baldwin M A. Bioinformatic methods to exploit mass spectrometric data for proteomic applications. Methods Enzymol, 2005, 402: [38] He Q Y, Cao J, Liu X H, et al. DEPD: a novel database for differentially expressed proteins. Bioinformatics, 2005, 21 (18): [39] Ransohoff D F. Bias as a threat to the validity of cancer molecular-marker research. Nat Rev Cancer, 2005, 5(2): [40] Ransohoff D F. Rules of evidence for cancer molecularmarker discovery and validation. Nat Rev Cancer, 2004, 4 (4): [41] Taylor C F, Paton N W, Garwood K L, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol, 2003, 21(3): FGF8 WNT1 (isthmic organizer) Development Lmx1b Lmx1b Lmx1b Fgf8 Wnt1 (Pax2 Gbx2 En1/En2)

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