哺乳动物细胞质膜及乳腺癌变蛋白质组研究
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摘要
细胞质膜(PM)是细胞与环境直接接触的界面。镶嵌或连接于其中的蛋白质作为细胞的“门铃”与“门户”，是现有的70％的药物的靶标，因此细胞质膜蛋白质组的研究具有重要的理论与实际应用意义。然而，由于质膜蛋白质具有难溶、低丰度以及组成复杂等特点，是一项具有极大挑战性的研究。
首先，本文以鼠肝为材料，对质膜蛋白质组的研究进行了一系列的方法摸索。肝脏在人体的生命活动中具有非常重要的功能，是一个复杂性仅次于大脑的器官。分析其质膜蛋白质组将有助于对肝脏的认识和肝病的治疗。我们用蔗糖密度梯度离心法纯化质膜，优化出适合2DE分离膜蛋白的裂解液(含4％w／v CHAPS和1％NP-40等)和初步摸索出整合膜蛋白质的富集方法(氯仿和甲醇抽提，Na_2CO_3处理)。对用2DE和SDS-PAGE分离的蛋白质进行质谱鉴定，一共鉴定了175个非冗余蛋白质。其中9％的蛋白质功能未知，生物学分析发现四个未知蛋白质可能与肌肉营养不良等疾病有关。其次，为了鉴定低丰度、强疏水性整合质膜蛋白质，我们用Na_2CO_3处理，氯仿与甲醇抽提，以及质膜微区分离策略来富集这些蛋白质。通过2DE／1DE-MS／MS的技术路线分析，一共鉴定了457个非冗余蛋白质，其中23％的带有一个或一个以上跨膜区(TM)。在这457个蛋白质中，有53个与细胞通信相关。对这些鉴定的蛋白质进行emPAI分析，发现有50％的蛋白质的浓度低于0.1M，其中12％的蛋白质浓度比arginase 1和actin的低100倍。对鉴定蛋白质的理化性质分析，发现Na_2CO_3处理有利于碱性蛋白质研究，氯仿与甲醇有利于多跨膜区蛋白质研究，微区策略有利于低丰度蛋白质研究。再有，为了提高质膜的纯度，采用抗体磁珠免疫亲和纯化方法来纯化质膜。通过对4种富集方法的比较，找到了最佳的纯化方法。与密度梯度离心的结果相比，这种方法能将质膜的纯度提高3倍，线粒体的污染减少了2倍，内质网的污染几乎被去除。随后，我们优化了初质膜、磁珠以及抗体的用量，得到了适合蛋白质组研究的较少用量。对纯化的质膜蛋白质进行SDS-PAGE分析，质谱鉴定。
Plasma membrane (PM) constitutes the interface between cells and their external environment. The proteins embedded in this membrane work as the "doorbells" and "doorways" of the cells, and are the targets of about 70% of all known drugs. For these reasons, proteomic analysis of the plasma membrane is very important for theoretical and applied cytology and pharmacology. However, due to the low abundance, high hydrophobicity and the evidently complexity of PM proteins, it is very challenging to study.
First, we used mouse/rat liver as material, and looked for the methods for PM proteome research. The liver is one of the most important organs in the body, probably second only to the brain in organ complexity. Therefore, proteomic analysis of liver PM will be helpful to understand these physiology activities and treat liver disease. We isolated PM from mouse liver by sucrose density gradient centrifugation. The optimized lysis buffer containing 4% CHAPS and 1% NP-40 was obtained. The methods for integral membrane protein enrichment
were analyzed and better methods----chloroform/methanol
extraction and sodium carbonate treatment were found. The extracted PM proteins were separated by 2DE and SDS-PAGE, and submitted to MS identification. In all, 175 non-redundant proteins were identified, of which 9% proteins with unknown function. Through prediction, four unknown proteins were found to be related with limb-girdle muscular dystrophy 2B, and so on. Second, in order to characterize low copy integral membrane proteins. Integral plasma membrane proteins were enriched through the treatment with 0. 1M Na_2CO_3, chloroform/methanol
首先，本文以鼠肝为材料，对质膜蛋白质组的研究进行了一系列的方法摸索。肝脏在人体的生命活动中具有非常重要的功能，是一个复杂性仅次于大脑的器官。分析其质膜蛋白质组将有助于对肝脏的认识和肝病的治疗。我们用蔗糖密度梯度离心法纯化质膜，优化出适合2DE分离膜蛋白的裂解液(含4％w／v CHAPS和1％NP-40等)和初步摸索出整合膜蛋白质的富集方法(氯仿和甲醇抽提，Na_2CO_3处理)。对用2DE和SDS-PAGE分离的蛋白质进行质谱鉴定，一共鉴定了175个非冗余蛋白质。其中9％的蛋白质功能未知，生物学分析发现四个未知蛋白质可能与肌肉营养不良等疾病有关。其次，为了鉴定低丰度、强疏水性整合质膜蛋白质，我们用Na_2CO_3处理，氯仿与甲醇抽提，以及质膜微区分离策略来富集这些蛋白质。通过2DE／1DE-MS／MS的技术路线分析，一共鉴定了457个非冗余蛋白质，其中23％的带有一个或一个以上跨膜区(TM)。在这457个蛋白质中，有53个与细胞通信相关。对这些鉴定的蛋白质进行emPAI分析，发现有50％的蛋白质的浓度低于0.1M，其中12％的蛋白质浓度比arginase 1和actin的低100倍。对鉴定蛋白质的理化性质分析，发现Na_2CO_3处理有利于碱性蛋白质研究，氯仿与甲醇有利于多跨膜区蛋白质研究，微区策略有利于低丰度蛋白质研究。再有，为了提高质膜的纯度，采用抗体磁珠免疫亲和纯化方法来纯化质膜。通过对4种富集方法的比较，找到了最佳的纯化方法。与密度梯度离心的结果相比，这种方法能将质膜的纯度提高3倍，线粒体的污染减少了2倍，内质网的污染几乎被去除。随后，我们优化了初质膜、磁珠以及抗体的用量，得到了适合蛋白质组研究的较少用量。对纯化的质膜蛋白质进行SDS-PAGE分析，质谱鉴定。
Plasma membrane (PM) constitutes the interface between cells and their external environment. The proteins embedded in this membrane work as the "doorbells" and "doorways" of the cells, and are the targets of about 70% of all known drugs. For these reasons, proteomic analysis of the plasma membrane is very important for theoretical and applied cytology and pharmacology. However, due to the low abundance, high hydrophobicity and the evidently complexity of PM proteins, it is very challenging to study.
First, we used mouse/rat liver as material, and looked for the methods for PM proteome research. The liver is one of the most important organs in the body, probably second only to the brain in organ complexity. Therefore, proteomic analysis of liver PM will be helpful to understand these physiology activities and treat liver disease. We isolated PM from mouse liver by sucrose density gradient centrifugation. The optimized lysis buffer containing 4% CHAPS and 1% NP-40 was obtained. The methods for integral membrane protein enrichment
were analyzed and better methods----chloroform/methanol
extraction and sodium carbonate treatment were found. The extracted PM proteins were separated by 2DE and SDS-PAGE, and submitted to MS identification. In all, 175 non-redundant proteins were identified, of which 9% proteins with unknown function. Through prediction, four unknown proteins were found to be related with limb-girdle muscular dystrophy 2B, and so on. Second, in order to characterize low copy integral membrane proteins. Integral plasma membrane proteins were enriched through the treatment with 0. 1M Na_2CO_3, chloroform/methanol
引文
[1] Hopkins AL, Groom CR: The drugggble genome. Nat Rev Drug Discov 2002, 1:727-730.
[2] Oh P, Li Y, Yu J, Durr E, Krasinska KM, Carver LA, Testa JE, Schnitzer JE: Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 2004, 429:629-635.
[3] Sprenger RR, Speijer D, Back JW, De Koster CG, Pannekoek H, Horrevoets AJ: Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis 2004, 25: 156-172.
[4] Santoni V, Rouquie D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, et al: Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J 1998, 16:633-641.
[5] Adam PJ, Boyd R, Tyson KL, Fletcher GC, Stamps A, Hudson L, Poyser HR, Redpath N, Griffiths M, Steers G, et al: Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J Biol Chem 2003, 278:6482-6489.
[6] Blonder J, Terunuma A, Conrads TP, Chan KC, Yee C, Lucas DA, Schaefer CF, Yu LR, Issaq HJ, Veenstra TD, Vogel JC: A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol 2004, 123:691-699.
[7] Rahbar AM, Fenselau C: Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins. J Proteome Res 2004, 3:1267-1277.
[8] 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.
[9] Morre DM, Morre DJ: Aqueous two-phase partition applied to the isolation of plasma membranes and Golgi apparatus from cultured mammalian cells. J Chromatogr B Biomed Sci Appl 2000, 743:377-387.
[10] Cap R, Li X, Liu Z, Peng X, Hu W, Wang X, Chen P, Xie J, Liang S: Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J Proteome Res 2006, 5:634-642.
[11] Zhao Y, Zhang W, Kho Y, Zhao Y: Proteomic analysis of integral plasma membrane proteins. Anal Chem 2004, 76:1817-1823.
[12] Zhang W, Zhou G, Zhao Y, White MA, Zhao Y: Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis 2003, 24:2855-2863.
[13] Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP: Expression profiling of lymphocyte plasma membrane proteins. Mol Ceil Proteomics 2004, 3:56-65.
[14] Raimondo F, Ceppi P, Guidi K, Masserini M, Foletti C, Pitto M: Proteomics of plasma membrane microdomains. Expert Rev Proteomics 2005, 2:793-807.
[15] Smart EJ, Ying YS, Mineo C, Anderson RG: A detergent-free method for purifying??caveolae membrane from tissue culture cells. Proc Natl Acad Sci U S A 1995, 92:10104-10108.
[16] Singer SJ, Nicolson GL: The structure and chemistry of mammalian cell membranes. Am J Pathol 1971, 65:427-437.
[17] Watt SA, Wilke A, Patschkowski T, Niehaus K: Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics 2005, 5:153-167.
[18] Santoni V, Kieffer S, Desclaux D, Masson F, Rabilloud T: Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 2000, 21:3329-3344.
[19] Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H, Ephritikhine G: Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Mol Cell Proteomics 2004, 3:675-691.
[20] Luche S, Santoni V, Rabilloud T: Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics 2003, 3:249-253.
[21] Zhang L, Xie J, Wang X, Liu X, Tang X, Cao R, Hu W, Nie S, Fan C, Liang S: Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins. Proteomics 2005, 5:4510-4524.
[22] Navarre C, Degand H, Bennett KL, Crawford JS, Mortz E, Boutry M: Subproteomics: identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae. Proteomics 2002, 2:1706-1714.
[23] Coughenour HD, Spaulding RS, Thompson CM: The synaptic vesicle proteome: a comparative study in membrane protein identification. Proteomics 2004, 4:3141-3155.
[24] van Montfort BA, Canas B, Duurkens R, Godovac-Zimmermann J, Robillard GT: Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mass Spectrom 2002, 37:322-330.
[25] van Montfort BA, Doeven MK, Canas B, Veenhoff LM, Poolman B, Robillard GT: Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry. Biochim Biophys Acta 2002, 1555:111-115.
[26] Zischka H, Gloeckner CJ, Klein C, Willmann S, Swiatek-de Lange M, Ueffing M: Improved mass spectrometric identification of gel-separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction. Proteomics 2004, 4:3776-3782.
[27] Springer DL, Auberry DL, Ahram M, Adkins JN, Feldhaus JM, Wahl JH, Wunschel DS, Rodland KD: Characterization of plasma membrane proteins from ovarian cancer cells using mass spectrometry. Dis Markers 2003, 19:219-228.
[28] Blonder J, Goshe MB, Moore RJ, Pasa-Tolic L, Masselon CD, Lipton MS, Smith RD: Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry, J Proteome Res 2002, 1:351-360.[29] Blonder J, Conrads TP, Yu LR, Terunuma A, Janini GM, Issaq HJ, Vogel JC, Veenstra TD: A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 2004, 4:31-45.
[30] Man P, NovakP, Cebecauer M, Horvath O, Fiserova A, Havlicek V, Bezouska K: Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells. Proteomics 2005, 5:113-122.
[31] Nielsen PA, Olsen JY, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR: Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 2005, 4:402-408.
[32] Foster LJ, De Hoog CL, Mann M: Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A 2003, 100:5813-5818.
[33] Prokai L, Zharikova AD, Stevens SM, Jr.: Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry. J Mass Spectrom 2005, 40:169-175.
[34] Imam-Sghiouar N, Laude-komaire I, Labas V, Pflieger D, Le Caer JP, Caron M, Nabias DK, Joubert-Caron R: Subproteomics analysis of phosphorylated proteins: application to the study of B-lymphoblasts from a patient with Scott syndrome. Proteomics 2002, 2:828-838.
[35] Nuhse TS, Stensballe A, Jensen ON, Peck SC: Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 2004, 16:2394-2405.
[36] Schindler J, Lewandrowski U, Sickmann A, Friauf E, Gerd Nothwang H: Proteomic Analysis of Brain Plasma Membranes Isolated by Affinity Two-phase Partitioning. Mol Cell Proteomics 2006, 5:390-400.
[37] Watarai H, Hinohara A, Nagafune J, Nakayama T, Taniguchi M, Yamaguchi Y: Plasma membrane-focused proteomics: dramatic changes in surface expression during the maturation of human dendritic cells. Proteomics 2005, 5:4001-4011.
[38] Zheng J, Gao X, Beretta L, He F: The Human Liver Proteome Project (HLPP) Workshop during the 4(th) HUPO World Congress. Proteomics 2006, 6:1716-1718.
[39] Rethy A, Trevisani A, Manservigi R, Tomasi V: Isolation and characterization of the plasma membrane from Yoshida hepatoma cells. J Membr Biol 1975, 20:99-110.
[40] Henningsen R, Gale BL, Stranb KM, DeNagel DC: Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry. Proteomics 2002, 2:1479-1488.
[41] Ferro M, Seigneurin-Berny D, Rolland N, Chapel A, Salvi D, Garin J, Joyard J: Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins. Electrophoresis 2000, 21:3517-3526.
[42] Klein JB, Gozal D, Pierce WM, Thongboonkerd V, Scherzer JA, Sachleben LR, Guo SZ, Cai J, Gozal E: Proteomic identification of a novel protein regulated in CA1 and CA3 hippocampal regions during intermittent hypoxia. Respir Physiol??Neurobiol 2003, 136:91-103.
[43] Bjellqvist B, Sanchez JC, Pasquali C, Ravier F, Paquet N, Frutiger S, Hughes GJ, Hochstrasser D: Micropreparative two-dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins. Electrophoresis 1993, 14:1375-1378.
[44] Schupbach J, Ammann RW, Freiburghaus AU: A universal method for two-dimensional polyacrylamide gel electrophoresis of membrane proteins using isoelectric focusing on immobilized pH gradients in the first dimension. Anal Biochem 1991, 196:337-343.
[45] Hellman U, Wernstedt C, Gonez J, Heldin CH: Improvement of an "In-Gel" digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal Biochem 1995, 224:451-455.
[46] Perkins DN, Pappin DJ, Creasy DM, Cottre11 JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
[47] Hirokawa T, Boon-Chieng S, Mitaku S: SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998, 14:378-379.
[48] Nakai K, Horton P: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999, 24:34-36.
[49] Pedersen SK, Harry JL, Sebastian L, Baker J, Traini MD, McCarthy JT, Manoharan A, Wilkins MR, Gooley AA, Righetti PG, et al: Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins. J Proteome Res 2003, 2:303-311.
[50] Borner GH, Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, Macaskill A, Napier JA, Beale MH, Lilley KS, Dupree P: Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol 2005, 137:104-116.
[51] Gobom J, Schuerenberg M, Mueller M, Theiss D, Lehrach H, Nordhoff E: Alpha-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem 2001, 73:434-438.
[52] Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et at: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
[53] Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
[54] Liu H, Sadygov RG, Yates JR, 3rd: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
[55] Jiang XS, Zhou H, Zhang L, Sheng QH, Li SJ, Li L, Hao P, Li YX, Xia QC, Wu JR, Zeng R: A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol??Cell Proteomics 2004, 3:441-455.
[56] Luers GH, Hartig R, Mohr H, Hausmann M, Fahimi HD, Cremer C, Volkl A: Immano-isolation of highly purified peroxisomes using magnetic beads and continuous immunomagnetic sorting. Electrophoresis 1998, 19:1205-1210.
[57] Kikuchi M, Hatano N, Yokota S, Shimozawa N, Imanaka T, Taniguchi H: Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. J Biol Chem 2004, 279:421-428.
[58] Calhoun BC, Goldenring JR: Two Rab proteins, vesicle-associated membrane protein 2 (VAMP-2) and secretory carrier membrane proteins (SCAMPs), are present on immunoisolated parietal cell tubulovesicles. Biochem J 1997, 325 (Pt 2):559-564.
[59] Srinivasan S, Traini M, Herbert B, Sexton D, Harry J, Alexander H, Williams KL, Alexander S: Proteomic analysis of a developmentally regulated secretory vesicle. Proteomics 2001, 1:1119-1127.
[60] Henley JR, McNiven MA: Association of a dynamin-like protein with the Golgi apparatus in mammalian cells, J Cell Biol 1996, 133:761-775.
[61] Morciano M, Burre J, Corvey C, Karas M, Zimmermann H, Volknandt W: Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis. J Neurochem 2005, 95:1732-1745.
[62] Simion FA, Fleischer B, Fleischer S: Two distinct mechanisms for taurocholate uptake in subcellular fractions from rat liver. J Biol Chem 1984, 259:10814-10822.
[63] Rajalingam K, Wunder C, Brinkmann V, Churin Y, Hekman M, Sievers C, Rapp UR, Rudel T: Prohibitin is required for Ras-induced Raf-MEK-ERK activation and epithelial cell migration. Nat Cell Biol 2005, 7:837-843.
[64] Buechler C, Bodzioch M, Bared SM, Sigruener A, Boettcher A, Lapicka-Bodzioch K, Aslanidis C, Duong CQ, Grandl M, Langmann T, et al: Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1. Genomics 2004, 83:1116-1124.
[65] Chan AT, Teo PM, Johnson PJ: Controversies in the management of locoregionally advanced nasopharyngeal carcinoma. Curr Opin Oncol 1998, 10:219-225.
[66] Chan AS, To KF, Lo KW, Mak KF, Pak W, Chiu B, Tse GM, Ding M, Li X, Lee JC, Huang DP: High frequency of chromosome 3p deletion in histologically normal nasopharyngeal epithelia from southern Chinese. Cancer Res 2000, 60:5365-5370.
[67] Raab-Traub N: Epstein-Barr virus in the pathogenesis of NPC. Semin Cancer Biol 2002, 12:431-441.
[68] Lominadze G, Rane MJ, Merchant M, Cai J, Ward RA, McLeish KR: Myeloid-related protein-14 is a p38 MAPK substrate in human neutrophils. J Immunol 2005, 174:7257-7267.
[69] Jia WH, Feng BJ, Xu ZL, Zhang XS, Huang P, Huang LX, Yu XJ, Feng QS, Yao MH, Shugart YY, Zeng YX: Familial risk and clustering of nasopharyngeal carcinoma in Guangdong, China. Cancer 2004, 101:363-369.
[70] Zhang B, Nie X, Xiao B, Xiang J, Shen S, Gong J, Zhou M, Zhu S, Zhou J, Qian??J, et al: Identification of tissue-specific genes in nasopharyngeal epithelial tissue and differentially expressed genes in nasopharyngeal carcinoma by suppression subtractive hybridization and cDNA microarray. Genes Chromosomes Cancer 2003, 38:80-90.
[71] Tan C, Li J, Wang J, Xiang Q, Zhang X, Dong L, Shen S, Liang S, Li G: Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection. Proteomics 2002, 2:306-312.
[72] Tan G, Heqing L, Jiangbo C, Ming J, Yanhong M, Xianghe L, Hong S, Li G: Apoptosis induced by low-dose paclitaxel is associated with p53 upregulation in nasopharyngeal carcinoma cells. Int J Cancer 2002, 97:168-172.
[73] Wu CC, Chien KY, Tsang NM, Chang KP, Hao SP, Tsao CH, Chang YS, Yu JS: Cancer cell-secreted proteomes as a basis for searching potential tumor markers: nasopharyngeal carcinoma as a model. Proteomics 2005, 5:3173-3182.
[74] Jiang PZ, Gan M, Huang H, Shen XM, Wang S, Yao KT: Proteomics-based identification of proteins with altered expression induced by 12-0-tetradecanoylphorbol 13-acetate in nasopharyngeal carcinoma CNE2 cells. Acta Biochim Biophys Sin (Shanghai) 2005, 37:97-106.
[75] Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, et al: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. NEngl J Med 2001, 344:783-792.
[76] Yeach RA, Liu D, Yao S, Chen Y, Liu XY, Downs S, Hawiger J:Receptor/transporter-independent targeting of functional peptides across the plasma membrane.J Biol Chem 2004, 279:11425-11431.
[77] Simpson RJ, Connolly LM, Eddes JS, Pereira JJ, Moritz RL, Reid GE: Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database. Electrophoresis 2000, 21:1707-1732.
[78] Vicandi B, Jimenez-Heffernan JA, Lopez-Ferrer P, Hardisson D, Perez-Campos A, Gonzalez-Peramato P, Viguer JM: Fine needle aspiration cytology of mammary carcinoma with osteoclast-like giant cells. Cytopathology 2004, 15:321-325.
[79] Svec A, Velenska Z: Renal epithelioid angiomyolipoma--a close mimic of renal cell carcinoma. Report of a case and review of the literature. Pathol Res Pract 2005, 200:851-856.
[80] He QY, Cao J, Liu XH, Li MX, Liu YS, Xie JY, Liang SP: DEPD: a novel database for differentially expressed proteins. Bioinformatics 2005, 21:3694-3696.
[81] Gonzalez-Moles MA, Esteban F, Bravo-Perez JJ, Bravo-Perez M, Ruiz-Avila I, Gil-Montoya JA, Gonzalez-Moles S: Adhesion molecule CD44 expression in non-tumor epithelium adjacent to laryngeal cancer. Onkologie 2006, 29:9-13.
[82] Schmidt M, Schler G, Gruensfelder P, Hoppe F: Differential gene expression in a paclitaxel-resistant clone of a head and neck cancer cell line. Eur Arch Otorhinolaryngol 2006, 263:127-134.
[83] Antonucci F, Chilosi M, Parolini C, Hamdan M, Astner H, Righetti PG: Two-dimensional molecular profiling of mantle cell lymphoma. Electrophoresis 2003, 24:2376-2385.[84] Verrier F, Mignotte B, Jan G, Brenner C: Study of PTPC composition during apoptosis for identification of viral protein target. Ann N Y Acad Sci 2003, 1010:126-142.
[85] Huang Y, Boskovic G, Niles RM: Retinoic acid-induced AP-1 transcriptional activity regulates B16 mouse melanoma growth inhibition and differentiation.J Ce11 Physiol 2003, 194:162-170.
[86] Guillemin MC, Raffoux E, Vitoux D, Kogan S, Soilihi H, Lallemand-Breitenbach V, Zhu J, Janin A, Daniel MT, Gourmel B, et al: In vivo activation of cAMP signaling induces growth arrest and differentiation in acute promyelocytic leukemia. J Exp Med 2002, 196:1373-1380.
[87] Ortiz MA, Bayon Y, Lopez-Hernandez FJ, Piedrafita FJ: Retinoids in combination therapies for the treatment of cancer: mechanisms and perspectives. Drug Resist Updat 2002, 5:162-175.
[88] Shimonishi T, Miyazaki K, Kono N, Sabit H, Tuneyama K, Harada K, Hirabayashi J, Kasai K, Nakanuma Y: Expression of endogenous galectin-1 and galectin-3 in intrahepatic cholangiocarcinoma. Hum Pathol 2001, 32:302-310.
[89] Fouillit M, Joubert-Caron R, Poirier F, Bourin P, Monostori E, Levi-Strauss M, Raphael M, Bladier D, Caron M: Regulation of CD45-induced signaling by galectin-1 in Burkitt lymphoma B cells. Glycobiology 2000, 10:413-419.
[90] Gires O, Andratschke M, Schmitt B, Mack B, Schaffrik M: Cytokeratin 8 associates with the external leaflet of plasma membranes in tumour cells. Biochem Biophys Res Commun 2005, 328:1154-1162.
[91] Dowsett M, Cooke T, Ellis I, Gullick WJ, Gusterson B, Mallon E, Walker R: Assessment of HER2 status in breast cancer: why, when and how? Eur J Cancer 2000, 36:170-176.
[92] Alaiya AA, Franzen B, Auer G, Linder S: Cancer proteomics: from identification of novel markers to creation of artifical learning models for tumor classification. Electrophoresis 2000, 21:1210-1217.
[93] Rai AJ, Stemmer PM, Zhang Z, Adam BL, Morgan WT, Caffrey RE, Podust VN, Patel M, Lim LY, Shipulina NV, et at: Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers. Proteomics 2005, 5:3467-3474.
[94] Somiari RI, Somiari S, Russell S, Shriver CD: Proteomics of breast carcinoma.J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815:215-225.
[95] Cells JE, Moreira JM, Gromova I, Cabezon T, Ralfkiaer U, Guldberg P, Straten PT, Mouridsen H, Friis E, Holm D, et al: Towards discovery-driven translational research in breast cancer. Febs J 2005, 272:2-15.
[96] Posadas EM, Simpkins F, Liotta LA, MacDonald C, Kohn EC: Proteomic analysis for the early detection and rational treatment of cancer--realistic hope? Ann Oncol 2005, 16:16-22.
[97] Czerwenka KF, Manavi M, Hosmann J, Jelincic D, Pischinger KI, Battistutti WB, Behna M, Kubista E: Comparative analysis of two-dimensional protein patterns??in malignant and normal human breast tissue. Cancer Detect Prey 2001, 25:268-279.
[98] Dupont M, Pages JM, Lafitte D, Siroy A, Boiler C: Identification of an OprD homologue in Acinetobacter baumannii, J Proteome Res 2005, 4:2386-2390.
[99] Seddighzadeh M, Linder S, Shoshan MC, Auer G, Alaiya AA: Inhibition of extracellular signal-regulated kinase 1/2 activity of the breast cancer cell Iine MDA-MB-231 leads to major alterations in the pattern of protein expression. Electrophoresis 2000, 21:2737-2743.
[100] Huber M, Bahr I, Kratzschmar JR, Becket A, Muller EC, Donner P, Pohlenz HD, Schneider MR, Sommer A: Comparison of proteomic and genomic analyses of the human breast cancer cell line T47D and the antiestrogen-resistant derivative T47D-r. Mol Cell Proteomics 2004, 3:43-55.
[101] Cowherd SM, Espina VA, Petricoin EF, 3rd, Liotta LA: Proteomic analysis of human breast cancer tissue with laser-capture microdissection and reverse-phase protein microarrays. Clin Breast Cancer 2004, 5:385-392.
[102] Zang L, Palmer Toy D, Hancock WS, Sgroi DC, Karger BL: Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 160/180 isotopic labeling, J Proteome Res 2004, 3:604-612.
[103] Fuller AP, Palmer-Toy D, Erlander MG, Sgroi DC: Laser capture microdissection and advanced molecular analysis of human breast cancer. J Mammary Gland Biol Neoplasia 2003, 8:335-345.
[104] Espina V, Dettloff KA, Cowherd S, Petricoin EF, 3rd, Liotta LA: Use of proteomic analysis to monitor responses to biological therapies. Expert Opin Biol Ther 2004, 4:83-93.
[105] Wu SL, Hancock WS, Goodrich GG, Kunitake ST: An approach to the proteomic analysis of a breast cancer cell line (SKBR-3). Proteomics 2003, 3:1037-1046.
[106] Jain KK: Applications of proteomics in oncology. Pharmacogenomics 2000, 1:385-393.
[107] Kurebayashi J: [Biomarkers in breast cancer]. Gan To Kagaku Ryoho 2004, 31:1021-1026.
[108] Callesen AK, Mohammed S, Bunkenborg J, Kruse TA, Cold S, Mogensen O, Christensen R, Vach W, Jorgensen PE, Jensen ON: Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 2005, 19:1578-1586.
[109] Moody TW, Dudek J, Zakowicz H, Walters J, Jensen RT, Petricoin E, Couldrey C, Green JE: VIP receptor antagonists inhibit mammary carcinogenesis in C3(1)SV40T antigen mice. Life Sci 2004, 74:1345-1357.
[110] Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD: Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J Biomol Tech 2004, 15:238-248.
[111] Govorukhina NI, Keizer-Gunnink A, van der Zee AG, de Jong S, de Bruijn HW, Bischoff R: Sample preparation of human serum for the analysis of tumor markers. Comparison of different approaches for albumin and gamma-globulin depletion. J Chromatogr A 2003, 1009:171-178.
[112] Alexander H, Stegner AL, Wagner-Mann C, Du Bois GC, Alexander S, Sauter ER:??Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res 2004, 10:7500-7510.
[113] Sauter ER, Shan S, Hewett JE, Speckman P, Du Bois GC: Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS. Int J Cancer 2005, 114:791-796.
[114] Sauter ER, Zhu W, Fan XJ, Wassell RP, Chervoneva I, Du Bois GC: Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer. Br J Cancer 2002, 86:1440-1443.
[115] Escobar MA, Hoelz DJ, Sandoval JA, Hickey RJ, Grosfeld JL, Malkas LH: Profiling of nuclear extract proteins from human neuroblastoma cell lines: the search forfingerprints. J Pediatr Surg 2005, 40:349-358.
[116] Luftner D, Possinger K: Nuclear matrix proteins as biomarkers for breast cancer. Expert Rev Mol Diagn 2002, 2:23-31.
[117] Wulfkuhle JD, Sgroi DC, Krutzsch H, Mclean K, McGarvey K, Knowlton M, Chen S, Shu H, Sahin A, Kurek R, et al: Proteomics of human breast ductal carcinoma in situ. Cancer Res 2002, 62:6740-6749.
[118] Somiari RI, Sullivan A, Russell S, Somiari S, Hu H, Jordan R, George A, Katenhusen R, Buchowiecka A, Arciero C, et al: High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast. Proteomics 2003, 3:1863-1873.
[119] Bisca A, D' Ambrosio C, Scaloni A, Puglisi F, Aprile G, Piga A, Zuiani C, Bazzocchi M, Di Loreto C, Paron I, et al: Proteomic evaluation of core biopsy specimens from breast lesions. Cancer Lett 2004, 204:79-86.
[120] Hathout Y, Gehrmann ML, Chertov A, Fenselau C: Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett 2004, 210:245-253.
[121] Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M: Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1:377-396.
[122] Julka S, Regnier F: Quantification in proteomics through stable isotope coding: a review. J Proteome Res 2004, 3:350-363.
[123] Paweletz CP, Trock B, Pennanen M, Tsangaris T, Magnant C, Liotta LA, Petricoin EF, 3rd: Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis Markers 2001, 17:301-307.
[124] Vlahou A, Laronga C, Wilson L, Gregory B, Fournier K, McGaughey D, Perry RR, Wright GL, Jr., Semmes OJ: A novel approach toward development of a rapid blood test for breast cancer. Clin Breast Cancer 2003, 4:203-209.
[125] Hudelist G, Pacher-Zavisin M, Singer CF, Holper T, Kubista E, Schreiber M, Manavi M, Bilban M, Czerwenka K: Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Res Treat 2004, 86:281-291.
[126] Torhorst J, Bucher C, Kononen J, Haas P, Zuber M, Kochli OR, Mross F, Dieterich H, Moch H, Mihatsch M, et al: Tissue microarrays for rapid linking of molecular changes to clinical endpoints. Am J Pathol 2001, 159:2249-2256.
[127] Vercoutter-Edouart AS, Lemoine J, Le Bourhis X, Louis H, Boilly B, Nurcombe V,??Revillion F, Peyrat JP, Hondermarck H: Proteomic analysis reveals that 14-3-3sigma is down-regulated in human breast cancer cells. Cancer Res 2001, 61:76-80.
[128] Nikolsky Y, Ekins S, Nikolskaya T, Bugrim A: A novel method for generation of signature networks as biomarkers from complex high throughput data. Toxicol Lett 2005, 158:20-29.
[129] Helzlsouer KJ, Couzi R: Hormones and breast cancer. Cancer 1995, 76:2059-2063.
[130] Feigelson HS, Henderson BE: Estrogens and breast cancer. Carcinogenesis 1996, 17:2279-2284.
[131] Natrajan PK, Soumakis K, Gambrell RD, Jr.: Estrogen replacement therapy in women with previous breast cancer. Am J Obstet Gynecol 1999, 181:288-295.
[132] Dixon JM, Jackson J, Renshaw L, Miller WR: Neoadjuvant tamoxifen and aromatase inhibitors: comparisons and clinical outcomes. J Steroid Biochem Mol Biol 2003, 86:295-299.
[133] Isaksson E, Wang H, Sahlin L, von Schoultz B, Cline JM, von Schoultz E: Effects of long-term HRT and tamoxifen on the expression of progesterone receptors A and B in breast tissue from surgically postmenopausal cynomolgus macaques. Breast Cancer Res Treat 2003, 79:233-239.
[134] Dimitrakakis C, Zhou J, Wang J, Belanger A, LaBrie F, Cheng C, Powell D, Bondy C: A physiologic role for testosterone in limiting estrogenic stimulation of the breast. Menopause 2003, 10:292-298.
[135] Zhang J, Sun Y, Liu ~, Sun Y, Liao DJ: Synergistic effects of androgen and estrogen on the mouse uterus and mammary gland. Oncol Rep 2004, 12:709-716.
[136] Watson PA, Kim K, Chen KS, Gould MN: Androgen-dependent mammary carcinogenesis in rats transgenic for the Neu proto-oncogene. Cancer Cell 2002, 2:67-79.
[137] Zhang L, Liu X, Zhang J, Cao R, Lin Y, Xie J, Chen P, Sun Y, Li D, Liang S: Proteome analysis of combined effects of androgen and estrogen on the mouse mammary gland. Proteomics 2006, 6:487-497.
[138] Pucci-Minafra I, Fontana S, Cancemi P, Alaimo G, Minafra S: Proteomic patterns of cultured breast cancer cells and epithelial mammary cells. Ann N Y Acad Sci 2002, 963:122-139.
[139] Adam PJ, Berry J, Loader JA, Tyson KL, Craggs G, Smith P, De Belin J, Steers G, Pezzella F, Sachsenmeir KF, et at: Arylamine N-acetyltransferase-1 is highly expressed in breast cancers and conveys enhanced growth and resistance to etoposide in vitro. Mol Cancer Res 2003, 1:826-835.
[140] Clarke R, Liu MC, Bouker KB, Gu Z, Lee RY, Zhu Y, Skaar TC, Gomez B, O'Brien K, Wang Y, Hilakivi-Clarke LA: Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling. Oncogene 2003, 22:7316-7339.
[141] Liao DZ, Pantazis CG, Hou X, Li SA: Promotion of estrogen-induced mammary gland carcinogenesis by androgen in the male Noble rat: probable mediation by steroid receptors. Carcinogenesis 1998, 19:2173-2180.
[142] Chen P, Nie S, Mi W, Wang XC, Liang SP: De novo sequencing of tryptic peptides sulfonated by 4-sulfophenyl isothiocyanate for unambiguous protein identification using post-source decay matrix-assisted laser??desorption/ionization mass spectrometry, Rapid Commun Mass Spectrom 2004,18:191-198.
[2] Oh P, Li Y, Yu J, Durr E, Krasinska KM, Carver LA, Testa JE, Schnitzer JE: Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 2004, 429:629-635.
[3] Sprenger RR, Speijer D, Back JW, De Koster CG, Pannekoek H, Horrevoets AJ: Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis 2004, 25: 156-172.
[4] Santoni V, Rouquie D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, et al: Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J 1998, 16:633-641.
[5] Adam PJ, Boyd R, Tyson KL, Fletcher GC, Stamps A, Hudson L, Poyser HR, Redpath N, Griffiths M, Steers G, et al: Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J Biol Chem 2003, 278:6482-6489.
[6] Blonder J, Terunuma A, Conrads TP, Chan KC, Yee C, Lucas DA, Schaefer CF, Yu LR, Issaq HJ, Veenstra TD, Vogel JC: A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry. J Invest Dermatol 2004, 123:691-699.
[7] Rahbar AM, Fenselau C: Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins. J Proteome Res 2004, 3:1267-1277.
[8] 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.
[9] Morre DM, Morre DJ: Aqueous two-phase partition applied to the isolation of plasma membranes and Golgi apparatus from cultured mammalian cells. J Chromatogr B Biomed Sci Appl 2000, 743:377-387.
[10] Cap R, Li X, Liu Z, Peng X, Hu W, Wang X, Chen P, Xie J, Liang S: Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J Proteome Res 2006, 5:634-642.
[11] Zhao Y, Zhang W, Kho Y, Zhao Y: Proteomic analysis of integral plasma membrane proteins. Anal Chem 2004, 76:1817-1823.
[12] Zhang W, Zhou G, Zhao Y, White MA, Zhao Y: Affinity enrichment of plasma membrane for proteomics analysis. Electrophoresis 2003, 24:2855-2863.
[13] Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP: Expression profiling of lymphocyte plasma membrane proteins. Mol Ceil Proteomics 2004, 3:56-65.
[14] Raimondo F, Ceppi P, Guidi K, Masserini M, Foletti C, Pitto M: Proteomics of plasma membrane microdomains. Expert Rev Proteomics 2005, 2:793-807.
[15] Smart EJ, Ying YS, Mineo C, Anderson RG: A detergent-free method for purifying??caveolae membrane from tissue culture cells. Proc Natl Acad Sci U S A 1995, 92:10104-10108.
[16] Singer SJ, Nicolson GL: The structure and chemistry of mammalian cell membranes. Am J Pathol 1971, 65:427-437.
[17] Watt SA, Wilke A, Patschkowski T, Niehaus K: Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics 2005, 5:153-167.
[18] Santoni V, Kieffer S, Desclaux D, Masson F, Rabilloud T: Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 2000, 21:3329-3344.
[19] Marmagne A, Rouet MA, Ferro M, Rolland N, Alcon C, Joyard J, Garin J, Barbier-Brygoo H, Ephritikhine G: Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Mol Cell Proteomics 2004, 3:675-691.
[20] Luche S, Santoni V, Rabilloud T: Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics 2003, 3:249-253.
[21] Zhang L, Xie J, Wang X, Liu X, Tang X, Cao R, Hu W, Nie S, Fan C, Liang S: Proteomic analysis of mouse liver plasma membrane: use of differential extraction to enrich hydrophobic membrane proteins. Proteomics 2005, 5:4510-4524.
[22] Navarre C, Degand H, Bennett KL, Crawford JS, Mortz E, Boutry M: Subproteomics: identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae. Proteomics 2002, 2:1706-1714.
[23] Coughenour HD, Spaulding RS, Thompson CM: The synaptic vesicle proteome: a comparative study in membrane protein identification. Proteomics 2004, 4:3141-3155.
[24] van Montfort BA, Canas B, Duurkens R, Godovac-Zimmermann J, Robillard GT: Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mass Spectrom 2002, 37:322-330.
[25] van Montfort BA, Doeven MK, Canas B, Veenhoff LM, Poolman B, Robillard GT: Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry. Biochim Biophys Acta 2002, 1555:111-115.
[26] Zischka H, Gloeckner CJ, Klein C, Willmann S, Swiatek-de Lange M, Ueffing M: Improved mass spectrometric identification of gel-separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction. Proteomics 2004, 4:3776-3782.
[27] Springer DL, Auberry DL, Ahram M, Adkins JN, Feldhaus JM, Wahl JH, Wunschel DS, Rodland KD: Characterization of plasma membrane proteins from ovarian cancer cells using mass spectrometry. Dis Markers 2003, 19:219-228.
[28] Blonder J, Goshe MB, Moore RJ, Pasa-Tolic L, Masselon CD, Lipton MS, Smith RD: Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry, J Proteome Res 2002, 1:351-360.[29] Blonder J, Conrads TP, Yu LR, Terunuma A, Janini GM, Issaq HJ, Vogel JC, Veenstra TD: A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 2004, 4:31-45.
[30] Man P, NovakP, Cebecauer M, Horvath O, Fiserova A, Havlicek V, Bezouska K: Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells. Proteomics 2005, 5:113-122.
[31] Nielsen PA, Olsen JY, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR: Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 2005, 4:402-408.
[32] Foster LJ, De Hoog CL, Mann M: Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A 2003, 100:5813-5818.
[33] Prokai L, Zharikova AD, Stevens SM, Jr.: Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry. J Mass Spectrom 2005, 40:169-175.
[34] Imam-Sghiouar N, Laude-komaire I, Labas V, Pflieger D, Le Caer JP, Caron M, Nabias DK, Joubert-Caron R: Subproteomics analysis of phosphorylated proteins: application to the study of B-lymphoblasts from a patient with Scott syndrome. Proteomics 2002, 2:828-838.
[35] Nuhse TS, Stensballe A, Jensen ON, Peck SC: Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 2004, 16:2394-2405.
[36] Schindler J, Lewandrowski U, Sickmann A, Friauf E, Gerd Nothwang H: Proteomic Analysis of Brain Plasma Membranes Isolated by Affinity Two-phase Partitioning. Mol Cell Proteomics 2006, 5:390-400.
[37] Watarai H, Hinohara A, Nagafune J, Nakayama T, Taniguchi M, Yamaguchi Y: Plasma membrane-focused proteomics: dramatic changes in surface expression during the maturation of human dendritic cells. Proteomics 2005, 5:4001-4011.
[38] Zheng J, Gao X, Beretta L, He F: The Human Liver Proteome Project (HLPP) Workshop during the 4(th) HUPO World Congress. Proteomics 2006, 6:1716-1718.
[39] Rethy A, Trevisani A, Manservigi R, Tomasi V: Isolation and characterization of the plasma membrane from Yoshida hepatoma cells. J Membr Biol 1975, 20:99-110.
[40] Henningsen R, Gale BL, Stranb KM, DeNagel DC: Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry. Proteomics 2002, 2:1479-1488.
[41] Ferro M, Seigneurin-Berny D, Rolland N, Chapel A, Salvi D, Garin J, Joyard J: Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins. Electrophoresis 2000, 21:3517-3526.
[42] Klein JB, Gozal D, Pierce WM, Thongboonkerd V, Scherzer JA, Sachleben LR, Guo SZ, Cai J, Gozal E: Proteomic identification of a novel protein regulated in CA1 and CA3 hippocampal regions during intermittent hypoxia. Respir Physiol??Neurobiol 2003, 136:91-103.
[43] Bjellqvist B, Sanchez JC, Pasquali C, Ravier F, Paquet N, Frutiger S, Hughes GJ, Hochstrasser D: Micropreparative two-dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins. Electrophoresis 1993, 14:1375-1378.
[44] Schupbach J, Ammann RW, Freiburghaus AU: A universal method for two-dimensional polyacrylamide gel electrophoresis of membrane proteins using isoelectric focusing on immobilized pH gradients in the first dimension. Anal Biochem 1991, 196:337-343.
[45] Hellman U, Wernstedt C, Gonez J, Heldin CH: Improvement of an "In-Gel" digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal Biochem 1995, 224:451-455.
[46] Perkins DN, Pappin DJ, Creasy DM, Cottre11 JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
[47] Hirokawa T, Boon-Chieng S, Mitaku S: SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998, 14:378-379.
[48] Nakai K, Horton P: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999, 24:34-36.
[49] Pedersen SK, Harry JL, Sebastian L, Baker J, Traini MD, McCarthy JT, Manoharan A, Wilkins MR, Gooley AA, Righetti PG, et al: Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins. J Proteome Res 2003, 2:303-311.
[50] Borner GH, Sherrier DJ, Weimar T, Michaelson LV, Hawkins ND, Macaskill A, Napier JA, Beale MH, Lilley KS, Dupree P: Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol 2005, 137:104-116.
[51] Gobom J, Schuerenberg M, Mueller M, Theiss D, Lehrach H, Nordhoff E: Alpha-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem 2001, 73:434-438.
[52] Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et at: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
[53] Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
[54] Liu H, Sadygov RG, Yates JR, 3rd: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
[55] Jiang XS, Zhou H, Zhang L, Sheng QH, Li SJ, Li L, Hao P, Li YX, Xia QC, Wu JR, Zeng R: A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol??Cell Proteomics 2004, 3:441-455.
[56] Luers GH, Hartig R, Mohr H, Hausmann M, Fahimi HD, Cremer C, Volkl A: Immano-isolation of highly purified peroxisomes using magnetic beads and continuous immunomagnetic sorting. Electrophoresis 1998, 19:1205-1210.
[57] Kikuchi M, Hatano N, Yokota S, Shimozawa N, Imanaka T, Taniguchi H: Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. J Biol Chem 2004, 279:421-428.
[58] Calhoun BC, Goldenring JR: Two Rab proteins, vesicle-associated membrane protein 2 (VAMP-2) and secretory carrier membrane proteins (SCAMPs), are present on immunoisolated parietal cell tubulovesicles. Biochem J 1997, 325 (Pt 2):559-564.
[59] Srinivasan S, Traini M, Herbert B, Sexton D, Harry J, Alexander H, Williams KL, Alexander S: Proteomic analysis of a developmentally regulated secretory vesicle. Proteomics 2001, 1:1119-1127.
[60] Henley JR, McNiven MA: Association of a dynamin-like protein with the Golgi apparatus in mammalian cells, J Cell Biol 1996, 133:761-775.
[61] Morciano M, Burre J, Corvey C, Karas M, Zimmermann H, Volknandt W: Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis. J Neurochem 2005, 95:1732-1745.
[62] Simion FA, Fleischer B, Fleischer S: Two distinct mechanisms for taurocholate uptake in subcellular fractions from rat liver. J Biol Chem 1984, 259:10814-10822.
[63] Rajalingam K, Wunder C, Brinkmann V, Churin Y, Hekman M, Sievers C, Rapp UR, Rudel T: Prohibitin is required for Ras-induced Raf-MEK-ERK activation and epithelial cell migration. Nat Cell Biol 2005, 7:837-843.
[64] Buechler C, Bodzioch M, Bared SM, Sigruener A, Boettcher A, Lapicka-Bodzioch K, Aslanidis C, Duong CQ, Grandl M, Langmann T, et al: Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1. Genomics 2004, 83:1116-1124.
[65] Chan AT, Teo PM, Johnson PJ: Controversies in the management of locoregionally advanced nasopharyngeal carcinoma. Curr Opin Oncol 1998, 10:219-225.
[66] Chan AS, To KF, Lo KW, Mak KF, Pak W, Chiu B, Tse GM, Ding M, Li X, Lee JC, Huang DP: High frequency of chromosome 3p deletion in histologically normal nasopharyngeal epithelia from southern Chinese. Cancer Res 2000, 60:5365-5370.
[67] Raab-Traub N: Epstein-Barr virus in the pathogenesis of NPC. Semin Cancer Biol 2002, 12:431-441.
[68] Lominadze G, Rane MJ, Merchant M, Cai J, Ward RA, McLeish KR: Myeloid-related protein-14 is a p38 MAPK substrate in human neutrophils. J Immunol 2005, 174:7257-7267.
[69] Jia WH, Feng BJ, Xu ZL, Zhang XS, Huang P, Huang LX, Yu XJ, Feng QS, Yao MH, Shugart YY, Zeng YX: Familial risk and clustering of nasopharyngeal carcinoma in Guangdong, China. Cancer 2004, 101:363-369.
[70] Zhang B, Nie X, Xiao B, Xiang J, Shen S, Gong J, Zhou M, Zhu S, Zhou J, Qian??J, et al: Identification of tissue-specific genes in nasopharyngeal epithelial tissue and differentially expressed genes in nasopharyngeal carcinoma by suppression subtractive hybridization and cDNA microarray. Genes Chromosomes Cancer 2003, 38:80-90.
[71] Tan C, Li J, Wang J, Xiang Q, Zhang X, Dong L, Shen S, Liang S, Li G: Proteomic analysis of differential protein expression in human nasopharyngeal carcinoma cells induced by NAG7 transfection. Proteomics 2002, 2:306-312.
[72] Tan G, Heqing L, Jiangbo C, Ming J, Yanhong M, Xianghe L, Hong S, Li G: Apoptosis induced by low-dose paclitaxel is associated with p53 upregulation in nasopharyngeal carcinoma cells. Int J Cancer 2002, 97:168-172.
[73] Wu CC, Chien KY, Tsang NM, Chang KP, Hao SP, Tsao CH, Chang YS, Yu JS: Cancer cell-secreted proteomes as a basis for searching potential tumor markers: nasopharyngeal carcinoma as a model. Proteomics 2005, 5:3173-3182.
[74] Jiang PZ, Gan M, Huang H, Shen XM, Wang S, Yao KT: Proteomics-based identification of proteins with altered expression induced by 12-0-tetradecanoylphorbol 13-acetate in nasopharyngeal carcinoma CNE2 cells. Acta Biochim Biophys Sin (Shanghai) 2005, 37:97-106.
[75] Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, et al: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. NEngl J Med 2001, 344:783-792.
[76] Yeach RA, Liu D, Yao S, Chen Y, Liu XY, Downs S, Hawiger J:Receptor/transporter-independent targeting of functional peptides across the plasma membrane.J Biol Chem 2004, 279:11425-11431.
[77] Simpson RJ, Connolly LM, Eddes JS, Pereira JJ, Moritz RL, Reid GE: Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database. Electrophoresis 2000, 21:1707-1732.
[78] Vicandi B, Jimenez-Heffernan JA, Lopez-Ferrer P, Hardisson D, Perez-Campos A, Gonzalez-Peramato P, Viguer JM: Fine needle aspiration cytology of mammary carcinoma with osteoclast-like giant cells. Cytopathology 2004, 15:321-325.
[79] Svec A, Velenska Z: Renal epithelioid angiomyolipoma--a close mimic of renal cell carcinoma. Report of a case and review of the literature. Pathol Res Pract 2005, 200:851-856.
[80] He QY, Cao J, Liu XH, Li MX, Liu YS, Xie JY, Liang SP: DEPD: a novel database for differentially expressed proteins. Bioinformatics 2005, 21:3694-3696.
[81] Gonzalez-Moles MA, Esteban F, Bravo-Perez JJ, Bravo-Perez M, Ruiz-Avila I, Gil-Montoya JA, Gonzalez-Moles S: Adhesion molecule CD44 expression in non-tumor epithelium adjacent to laryngeal cancer. Onkologie 2006, 29:9-13.
[82] Schmidt M, Schler G, Gruensfelder P, Hoppe F: Differential gene expression in a paclitaxel-resistant clone of a head and neck cancer cell line. Eur Arch Otorhinolaryngol 2006, 263:127-134.
[83] Antonucci F, Chilosi M, Parolini C, Hamdan M, Astner H, Righetti PG: Two-dimensional molecular profiling of mantle cell lymphoma. Electrophoresis 2003, 24:2376-2385.[84] Verrier F, Mignotte B, Jan G, Brenner C: Study of PTPC composition during apoptosis for identification of viral protein target. Ann N Y Acad Sci 2003, 1010:126-142.
[85] Huang Y, Boskovic G, Niles RM: Retinoic acid-induced AP-1 transcriptional activity regulates B16 mouse melanoma growth inhibition and differentiation.J Ce11 Physiol 2003, 194:162-170.
[86] Guillemin MC, Raffoux E, Vitoux D, Kogan S, Soilihi H, Lallemand-Breitenbach V, Zhu J, Janin A, Daniel MT, Gourmel B, et al: In vivo activation of cAMP signaling induces growth arrest and differentiation in acute promyelocytic leukemia. J Exp Med 2002, 196:1373-1380.
[87] Ortiz MA, Bayon Y, Lopez-Hernandez FJ, Piedrafita FJ: Retinoids in combination therapies for the treatment of cancer: mechanisms and perspectives. Drug Resist Updat 2002, 5:162-175.
[88] Shimonishi T, Miyazaki K, Kono N, Sabit H, Tuneyama K, Harada K, Hirabayashi J, Kasai K, Nakanuma Y: Expression of endogenous galectin-1 and galectin-3 in intrahepatic cholangiocarcinoma. Hum Pathol 2001, 32:302-310.
[89] Fouillit M, Joubert-Caron R, Poirier F, Bourin P, Monostori E, Levi-Strauss M, Raphael M, Bladier D, Caron M: Regulation of CD45-induced signaling by galectin-1 in Burkitt lymphoma B cells. Glycobiology 2000, 10:413-419.
[90] Gires O, Andratschke M, Schmitt B, Mack B, Schaffrik M: Cytokeratin 8 associates with the external leaflet of plasma membranes in tumour cells. Biochem Biophys Res Commun 2005, 328:1154-1162.
[91] Dowsett M, Cooke T, Ellis I, Gullick WJ, Gusterson B, Mallon E, Walker R: Assessment of HER2 status in breast cancer: why, when and how? Eur J Cancer 2000, 36:170-176.
[92] Alaiya AA, Franzen B, Auer G, Linder S: Cancer proteomics: from identification of novel markers to creation of artifical learning models for tumor classification. Electrophoresis 2000, 21:1210-1217.
[93] Rai AJ, Stemmer PM, Zhang Z, Adam BL, Morgan WT, Caffrey RE, Podust VN, Patel M, Lim LY, Shipulina NV, et at: Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers. Proteomics 2005, 5:3467-3474.
[94] Somiari RI, Somiari S, Russell S, Shriver CD: Proteomics of breast carcinoma.J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815:215-225.
[95] Cells JE, Moreira JM, Gromova I, Cabezon T, Ralfkiaer U, Guldberg P, Straten PT, Mouridsen H, Friis E, Holm D, et al: Towards discovery-driven translational research in breast cancer. Febs J 2005, 272:2-15.
[96] Posadas EM, Simpkins F, Liotta LA, MacDonald C, Kohn EC: Proteomic analysis for the early detection and rational treatment of cancer--realistic hope? Ann Oncol 2005, 16:16-22.
[97] Czerwenka KF, Manavi M, Hosmann J, Jelincic D, Pischinger KI, Battistutti WB, Behna M, Kubista E: Comparative analysis of two-dimensional protein patterns??in malignant and normal human breast tissue. Cancer Detect Prey 2001, 25:268-279.
[98] Dupont M, Pages JM, Lafitte D, Siroy A, Boiler C: Identification of an OprD homologue in Acinetobacter baumannii, J Proteome Res 2005, 4:2386-2390.
[99] Seddighzadeh M, Linder S, Shoshan MC, Auer G, Alaiya AA: Inhibition of extracellular signal-regulated kinase 1/2 activity of the breast cancer cell Iine MDA-MB-231 leads to major alterations in the pattern of protein expression. Electrophoresis 2000, 21:2737-2743.
[100] Huber M, Bahr I, Kratzschmar JR, Becket A, Muller EC, Donner P, Pohlenz HD, Schneider MR, Sommer A: Comparison of proteomic and genomic analyses of the human breast cancer cell line T47D and the antiestrogen-resistant derivative T47D-r. Mol Cell Proteomics 2004, 3:43-55.
[101] Cowherd SM, Espina VA, Petricoin EF, 3rd, Liotta LA: Proteomic analysis of human breast cancer tissue with laser-capture microdissection and reverse-phase protein microarrays. Clin Breast Cancer 2004, 5:385-392.
[102] Zang L, Palmer Toy D, Hancock WS, Sgroi DC, Karger BL: Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 160/180 isotopic labeling, J Proteome Res 2004, 3:604-612.
[103] Fuller AP, Palmer-Toy D, Erlander MG, Sgroi DC: Laser capture microdissection and advanced molecular analysis of human breast cancer. J Mammary Gland Biol Neoplasia 2003, 8:335-345.
[104] Espina V, Dettloff KA, Cowherd S, Petricoin EF, 3rd, Liotta LA: Use of proteomic analysis to monitor responses to biological therapies. Expert Opin Biol Ther 2004, 4:83-93.
[105] Wu SL, Hancock WS, Goodrich GG, Kunitake ST: An approach to the proteomic analysis of a breast cancer cell line (SKBR-3). Proteomics 2003, 3:1037-1046.
[106] Jain KK: Applications of proteomics in oncology. Pharmacogenomics 2000, 1:385-393.
[107] Kurebayashi J: [Biomarkers in breast cancer]. Gan To Kagaku Ryoho 2004, 31:1021-1026.
[108] Callesen AK, Mohammed S, Bunkenborg J, Kruse TA, Cold S, Mogensen O, Christensen R, Vach W, Jorgensen PE, Jensen ON: Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 2005, 19:1578-1586.
[109] Moody TW, Dudek J, Zakowicz H, Walters J, Jensen RT, Petricoin E, Couldrey C, Green JE: VIP receptor antagonists inhibit mammary carcinogenesis in C3(1)SV40T antigen mice. Life Sci 2004, 74:1345-1357.
[110] Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD: Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J Biomol Tech 2004, 15:238-248.
[111] Govorukhina NI, Keizer-Gunnink A, van der Zee AG, de Jong S, de Bruijn HW, Bischoff R: Sample preparation of human serum for the analysis of tumor markers. Comparison of different approaches for albumin and gamma-globulin depletion. J Chromatogr A 2003, 1009:171-178.
[112] Alexander H, Stegner AL, Wagner-Mann C, Du Bois GC, Alexander S, Sauter ER:??Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res 2004, 10:7500-7510.
[113] Sauter ER, Shan S, Hewett JE, Speckman P, Du Bois GC: Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS. Int J Cancer 2005, 114:791-796.
[114] Sauter ER, Zhu W, Fan XJ, Wassell RP, Chervoneva I, Du Bois GC: Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer. Br J Cancer 2002, 86:1440-1443.
[115] Escobar MA, Hoelz DJ, Sandoval JA, Hickey RJ, Grosfeld JL, Malkas LH: Profiling of nuclear extract proteins from human neuroblastoma cell lines: the search forfingerprints. J Pediatr Surg 2005, 40:349-358.
[116] Luftner D, Possinger K: Nuclear matrix proteins as biomarkers for breast cancer. Expert Rev Mol Diagn 2002, 2:23-31.
[117] Wulfkuhle JD, Sgroi DC, Krutzsch H, Mclean K, McGarvey K, Knowlton M, Chen S, Shu H, Sahin A, Kurek R, et al: Proteomics of human breast ductal carcinoma in situ. Cancer Res 2002, 62:6740-6749.
[118] Somiari RI, Sullivan A, Russell S, Somiari S, Hu H, Jordan R, George A, Katenhusen R, Buchowiecka A, Arciero C, et al: High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast. Proteomics 2003, 3:1863-1873.
[119] Bisca A, D' Ambrosio C, Scaloni A, Puglisi F, Aprile G, Piga A, Zuiani C, Bazzocchi M, Di Loreto C, Paron I, et al: Proteomic evaluation of core biopsy specimens from breast lesions. Cancer Lett 2004, 204:79-86.
[120] Hathout Y, Gehrmann ML, Chertov A, Fenselau C: Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett 2004, 210:245-253.
[121] Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M: Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1:377-396.
[122] Julka S, Regnier F: Quantification in proteomics through stable isotope coding: a review. J Proteome Res 2004, 3:350-363.
[123] Paweletz CP, Trock B, Pennanen M, Tsangaris T, Magnant C, Liotta LA, Petricoin EF, 3rd: Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis Markers 2001, 17:301-307.
[124] Vlahou A, Laronga C, Wilson L, Gregory B, Fournier K, McGaughey D, Perry RR, Wright GL, Jr., Semmes OJ: A novel approach toward development of a rapid blood test for breast cancer. Clin Breast Cancer 2003, 4:203-209.
[125] Hudelist G, Pacher-Zavisin M, Singer CF, Holper T, Kubista E, Schreiber M, Manavi M, Bilban M, Czerwenka K: Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Res Treat 2004, 86:281-291.
[126] Torhorst J, Bucher C, Kononen J, Haas P, Zuber M, Kochli OR, Mross F, Dieterich H, Moch H, Mihatsch M, et al: Tissue microarrays for rapid linking of molecular changes to clinical endpoints. Am J Pathol 2001, 159:2249-2256.
[127] Vercoutter-Edouart AS, Lemoine J, Le Bourhis X, Louis H, Boilly B, Nurcombe V,??Revillion F, Peyrat JP, Hondermarck H: Proteomic analysis reveals that 14-3-3sigma is down-regulated in human breast cancer cells. Cancer Res 2001, 61:76-80.
[128] Nikolsky Y, Ekins S, Nikolskaya T, Bugrim A: A novel method for generation of signature networks as biomarkers from complex high throughput data. Toxicol Lett 2005, 158:20-29.
[129] Helzlsouer KJ, Couzi R: Hormones and breast cancer. Cancer 1995, 76:2059-2063.
[130] Feigelson HS, Henderson BE: Estrogens and breast cancer. Carcinogenesis 1996, 17:2279-2284.
[131] Natrajan PK, Soumakis K, Gambrell RD, Jr.: Estrogen replacement therapy in women with previous breast cancer. Am J Obstet Gynecol 1999, 181:288-295.
[132] Dixon JM, Jackson J, Renshaw L, Miller WR: Neoadjuvant tamoxifen and aromatase inhibitors: comparisons and clinical outcomes. J Steroid Biochem Mol Biol 2003, 86:295-299.
[133] Isaksson E, Wang H, Sahlin L, von Schoultz B, Cline JM, von Schoultz E: Effects of long-term HRT and tamoxifen on the expression of progesterone receptors A and B in breast tissue from surgically postmenopausal cynomolgus macaques. Breast Cancer Res Treat 2003, 79:233-239.
[134] Dimitrakakis C, Zhou J, Wang J, Belanger A, LaBrie F, Cheng C, Powell D, Bondy C: A physiologic role for testosterone in limiting estrogenic stimulation of the breast. Menopause 2003, 10:292-298.
[135] Zhang J, Sun Y, Liu ~, Sun Y, Liao DJ: Synergistic effects of androgen and estrogen on the mouse uterus and mammary gland. Oncol Rep 2004, 12:709-716.
[136] Watson PA, Kim K, Chen KS, Gould MN: Androgen-dependent mammary carcinogenesis in rats transgenic for the Neu proto-oncogene. Cancer Cell 2002, 2:67-79.
[137] Zhang L, Liu X, Zhang J, Cao R, Lin Y, Xie J, Chen P, Sun Y, Li D, Liang S: Proteome analysis of combined effects of androgen and estrogen on the mouse mammary gland. Proteomics 2006, 6:487-497.
[138] Pucci-Minafra I, Fontana S, Cancemi P, Alaimo G, Minafra S: Proteomic patterns of cultured breast cancer cells and epithelial mammary cells. Ann N Y Acad Sci 2002, 963:122-139.
[139] Adam PJ, Berry J, Loader JA, Tyson KL, Craggs G, Smith P, De Belin J, Steers G, Pezzella F, Sachsenmeir KF, et at: Arylamine N-acetyltransferase-1 is highly expressed in breast cancers and conveys enhanced growth and resistance to etoposide in vitro. Mol Cancer Res 2003, 1:826-835.
[140] Clarke R, Liu MC, Bouker KB, Gu Z, Lee RY, Zhu Y, Skaar TC, Gomez B, O'Brien K, Wang Y, Hilakivi-Clarke LA: Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling. Oncogene 2003, 22:7316-7339.
[141] Liao DZ, Pantazis CG, Hou X, Li SA: Promotion of estrogen-induced mammary gland carcinogenesis by androgen in the male Noble rat: probable mediation by steroid receptors. Carcinogenesis 1998, 19:2173-2180.
[142] Chen P, Nie S, Mi W, Wang XC, Liang SP: De novo sequencing of tryptic peptides sulfonated by 4-sulfophenyl isothiocyanate for unambiguous protein identification using post-source decay matrix-assisted laser??desorption/ionization mass spectrometry, Rapid Commun Mass Spectrom 2004,18:191-198.