Breast cancer proteomics: clinical perspectives

Bibliography

• LEVI F, LUCCHINI F, NEGRI E, LA VECCHIA C: Trends in mortality from major cancers in the European Union, including acceding countries, in 2004. Cancer (2004) 101(12):2843-2850.
   PubMed Web of Science ®Google Scholar
• BRENNAN DJ, O’BRIEN SL, FAGAN A et al.: Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opin. Biol. Ther. (2005) 5(8):1069-1083.
   PubMed Web of Science ®Google Scholar
• PEROU CM, SORLIE T, EISEN MB et al.: Molecular portraits of human breast tumours. Nature (2000) 406(6797):747-752.
   PubMed Web of Science ®Google Scholar
• ELMORE JG, ARMSTRONG K, LEHMAN CD, FLETCHER SW: Screening for breast cancer. JAMA (2005) 293(10):1245-1256.
   PubMed Web of Science ®Google Scholar
• MARIANI G: New developments in the treatment of metastatic breast cancer: from chemotherapy to biological therapy. Ann. Oncol. (2005) 16(Suppl. 2):ii191-ii194.
   PubMedGoogle Scholar
• NO AUTHORS LISTED: Polychemotherapy for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists’ Collaborative Group. Lancet (1998) 352(9132):930-942.
   PubMed Web of Science ®Google Scholar
• BALMAIN A, GRAY J, PONDER B: The genetics and genomics of cancer. Nat. Genet. (2003) 33(Suppl.):238-244.
   PubMed Web of Science ®Google Scholar
• PANDEY A, MANN M: Proteomics to study genes and genomes. Nature (2000) 405(6788):837-846.
   PubMed Web of Science ®Google Scholar
• ANDERSON L, SEILHAMER J: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis (1997) 18(3-4):533-537.
   PubMed Web of Science ®Google Scholar
• GORG A, WEISS W, DUNN MJ: Current two-dimensional electrophoresis technology for proteomics. Proteomics (2004) 4(12):3665-3685.
   PubMed Web of Science ®Google Scholar
• BERGGREN K, CHERNOKALSKAYA E, STEINBERG TH et al.: Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis (2000) 21(12):2509-2521.
   PubMed Web of Science ®Google Scholar
• WU J, LENCHIK NJ, PABST MJ et al.: Functional characterization of two-dimensional gel-separated proteins using sequential staining. Electrophoresis (2005) 26(1):225-237.
   PubMed Web of Science ®Google Scholar
• GE Y, RAJKUMAR L, GUZMAN RC et al.: Multiplexed fluorescence detection of phosphorylation, glycosylation, and total protein in the proteomic analysis of breast cancer refractoriness. Proteomics (2004) 4(11):3464-3467.
   PubMed Web of Science ®Google Scholar
• STEIN RC, ZVELEBIL MJ: The application of 2D gel-based proteomics methods to the study of breast cancer. J. Mammary Gland Biol. Neoplasia (2002) 7(4):385-393.
   PubMed Web of Science ®Google Scholar
• GHARBI S, GAFFNEY P, YANG A et al.: Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol. Cell. Proteomics (2002) 1(2):91-98.
   PubMed Web of Science ®Google Scholar
• AEBERSOLD R, MANN M: Mass spectrometry-based proteomics. Nature (2003) 422(6928):198-207.
   PubMed Web of Science ®Google Scholar
• WOLTERS DA, WASHBURN MP, YATES JR 3RD: An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. (2001) 73(23):5683-5690.
   PubMed Web of Science ®Google Scholar
• JENKINS RE, KITTERINGHAM NR, HUNTER CL et al.: Relative and absolute quantitative expression profiling of cytochromes P450 using isotope-coded affinity tags. Proteomics (2006) 6(6):1934-1947.
   PubMed Web of Science ®Google Scholar
• WU WW, WANG G, BAEK SJ, SHEN RF: Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res. (2006) 5(3):651-658.
   Google Scholar
• GEHRMANN ML, HATHOUT Y, FENSELAU C: Evaluation of metabolic labeling for comparative proteomics in breast cancer cells. J. Proteome Res. (2004) 3(5):1063-1068.
   Google Scholar
• BEYNON RJ, DOHERTY MK, PRATT JM, GASKELL SJ: Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods (2005) 2(8):587-589.
   PubMed Web of Science ®Google Scholar
• DIAMANDIS EP: Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol. Cell. Proteomics (2004) 3(4):367-378.
   Google Scholar
• HAAB BB: Antibody arrays in cancer research. Mol. Cell. Proteomics (2005) 4(4):377-383.
   Google Scholar
• SANCHEZ-CARBAYO M: Antibody arrays: technical considerations and clinical applications in cancer. Clin. Chem. (2006) 52(9):1651-1659.
   PubMed Web of Science ®Google Scholar
• UHLEN M, BJORLING E, AGATON C et al.: A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics (2005) 4(12):1920-1932.
   PubMed Web of Science ®Google Scholar
• EK S, ANDREASSON U, HOBER S et al.: From gene expression analysis to tissue microarrays: a rational approach to identify therapeutic and diagnostic targets in lymphoid malignancies. Mol. Cell. Proteomics (2006) 5(6):1072-1081.
   PubMed Web of Science ®Google Scholar
• JESSANI N, HUMPHREY M, MCDONALD WH et al.: Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo. Proc. Natl. Acad. Sci. USA (2004) 101(38):13756-13761.
   PubMed Web of Science ®Google Scholar
• NEUBAUER H, CLARE SE, KUREK R et al.: Breast cancer proteomics by laser capture microdissection, sample pooling, 54-cm IPG IEF, and differential iodine radioisotope detection. Electrophoresis (2006) 27(9):1840-1852.
   PubMed Web of Science ®Google Scholar
• 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 16O/18O isotopic labeling. J. Proteome Res. (2004) 3(3):604-612.
   PubMed Web of Science ®Google Scholar
• BISCA A, D’AMBROSIO C, SCALONI A et al.: Proteomic evaluation of core biopsy specimens from breast lesions. Cancer Lett. (2004) 204(1):79-86.
   PubMed Web of Science ®Google Scholar
• ALAIYA A, AL-MOHANNA M, LINDER S: Clinical cancer proteomics: promises and pitfalls. J. Proteome Res. (2005) 4(4):1213-1222.
   PubMed Web of Science ®Google Scholar
• ROSENBLATT KP, BRYANT-GREENWOOD P, KILLIAN JK et al.: Serum proteomics in cancer diagnosis and management. Annu. Rev. Med. (2004) 55:97-112.
   PubMed Web of Science ®Google Scholar
• LI J, ZHAO J, YU X et al.: Identification of biomarkers for breast cancer in nipple aspiration and ductal lavage fluid. Clin. Cancer Res. (2005) 11(23):8312-8320.
   PubMed Web of Science ®Google Scholar
• CELIS JE, GROMOV P, CABEZON T et al.: Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: a novel resource for biomarker and therapeutic target discovery. Mol. Cell. Proteomics (2004) 3(4):327-344.
   PubMed Web of Science ®Google Scholar
• CELIS JE, GROMOV P, MOREIRA JM et al.: Apocrine cysts of the breast: Biomarkers, origin, enlargement, and relation with cancer phenotype. Mol. Cell. Proteomics (2005) 3(4):327-344.
   Web of Science ®Google Scholar
• HU Y, ZHANG S, YU J, LIU J, ZHENG S: SELDI-TOF-MS: the proteomics and bioinformatics approaches in the diagnosis of breast cancer. Breast (2005) 14(4):250-255.
   PubMed Web of Science ®Google Scholar
• LI J, ZHANG Z, ROSENZWEIG J, WANG YY, CHAN DW: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem. (2002) 48(8):1296-1304.
   PubMed Web of Science ®Google Scholar
• VERCOUTTER-EDOUART AS, LEMOINE J, LE BOURHIS X et al.: Proteomic analysis reveals that 14-3-3sigma is down-regulated in human breast cancer cells. Cancer Res. (2001) 61(1):76-80.
   PubMed Web of Science ®Google Scholar
• FERGUSON AT, EVRON E, UMBRICHT CB et al.: High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer. Proc. Natl. Acad. Sci. USA (2000) 97(11):6049-6054.
   Google Scholar
• MOREIRA JM, OHLSSON G, RANK FE, CELIS JE: Down-regulation of the tumor suppressor protein 14-3-3sigma is a sporadic event in cancer of the breast. Mol. Cell. Proteomics (2005) 4(4):555-569.
   PubMed Web of Science ®Google Scholar
• PAWLIK TM, FRITSCHE H, COOMBES KR et al.: Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. Breast Cancer Res. Treat. (2005) 89(2):149-157.
   PubMed Web of Science ®Google Scholar
• PAWELETZ CP, TROCK B, PENNANEN M et al.: 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(4):301-307.
   PubMed Web of Science ®Google Scholar
• COOMBES KR, FRITSCHE HA JR, CLARKE C et al.: Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin. Chem. (2003) 49(10):1615-1623.
   PubMed Web of Science ®Google Scholar
• FUNG ET, YIP TT, LOMAS L et al.: Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int. J. Cancer (2005) 115(5):783-789.
   PubMed Web of Science ®Google Scholar
• HANAHAN D, WEINBERG RA: The hallmarks of cancer. Cell (2000) 100(1):57-70.
   PubMed Web of Science ®Google Scholar
• NAGARAJA GM, OTHMAN M, FOX BP et al.: Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics. Oncogene (2005) 25(16):2328-2338.
   Web of Science ®Google Scholar
• HATHOUT Y, GEHRMANN ML, CHERTOV A, FENSELAU C: Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett. (2004) 210(2):245-253.
   PubMed Web of Science ®Google Scholar
• GONCALVES A, ESTERNI B, BERTUCCI F et al.: Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene (2005) 25(7):981-989.
   Web of Science ®Google Scholar
• JACQUEMIER J, GINESTIER C, ROUGEMONT J et al.: Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res. (2005) 65(3):767-779.
   PubMed Web of Science ®Google Scholar
• HENDERSON IC, BERRY DA, DEMETRI GD et al.: Improved outcomes from adding sequential paclitaxel but not from escalating doxorubicin dose in an adjuvant chemotherapy regimen for patients with node-positive primary breast cancer. J. Clin. Oncol. (2003) 21(6):976-983.
   PubMed Web of Science ®Google Scholar
• SLAMON DJ, LEYLAND-JONES B, SHAK S et al.: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N. Engl. J. Med. (2001) 344(11):783-792.
   PubMed Web of Science ®Google Scholar
• BROWN KJ, FENSELAU C: Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shot-gun comparative proteomics with proteolytic 18O labeling. J. Proteome Res. (2004) 3(3):455-462.
   PubMed Web of Science ®Google Scholar
• FU Z, FENSELAU C: Proteomic evidence for roles for nucleolin and poly[ADP-ribosyl] transferase in drug resistance. J. Proteome Res. (2005) 4(5):1583-1591.
   PubMed Web of Science ®Google Scholar
• MIAN S, BALL G, HORNBUCKLE J et al.: A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to paclitaxel and doxorubicin under in vitro conditions. Proteomics (2003) 3(9):1725-1737.
   PubMed Web of Science ®Google Scholar
• DOWSETT M: Biomarker investigations from the ATAC trial: the role of TA01. Breast Cancer Res. Treat. (2004) 87(Suppl. 1):S11-S18.
   PubMed Web of Science ®Google Scholar
• NICHOLSON RI, JOHNSTON SR: Endocrine therapy-current benefits and limitations. Breast Cancer Res. Treat. (2005) 93(Suppl. 1):S3-S10.
   PubMed Web of Science ®Google Scholar
• BESADA V, DIAZ M, BECKER M et al.: Proteomics of xenografted human breast cancer indicates novel targets related to tamoxifen resistance. Proteomics (2005) 6(3):1038-1048.
   Web of Science ®Google Scholar
• REHMAN A, CHAHAL MS, TANG X et al.: Proteomic identification of heat shock protein 90 as a candidate target for p53 mutation reactivation by PRIMA-1 in breast cancer cells. Breast Cancer Res. (2005) 7(5):R765-R774.
   PubMed Web of Science ®Google Scholar
• ROWELL C, CARPENTER DM, LAMARTINIERE CA: Chemoprevention of breast cancer, proteomic discovery of genistein action in the rat mammary gland. J. Nutr. (2005) 135(12 Suppl.):2953S-2959S.
   PubMed Web of Science ®Google Scholar
• EFUET ET, KEYOMARSI K: Farnesyl and geranylgeranyl transferase inhibitors induce G1 arrest by targeting the proteasome. Cancer Res. (2006) 66(2):1040-1051.
   PubMed Web of Science ®Google Scholar
• CICENAS J, URBAN P, KUNG W et al.: Phosphorylation of tyrosine 1248-ERBB2 measured by chemiluminescence-linked immunoassay is an independent predictor of poor prognosis in primary breast cancer patients. Eur. J. Cancer (2006) 42(5):636-645.
   PubMed Web of Science ®Google Scholar
• WULFKUHLE JD, SGROI DC, KRUTZSCH H et al.: Proteomics of human breast ductal carcinoma in situ. Cancer Res. (2002) 62(22):6740-6749.
   PubMed Web of Science ®Google Scholar
• PUCCI-MINAFRA I, FONTANA S, CANCEMI P et al.: A contribution to breast cancer cell proteomics: detection of new sequences. Proteomics (2002) 2(7):919-927.
   PubMed Web of Science ®Google Scholar
• DOCQUIER F, FARRAR D, D’ARCY V et al.: Heightened expression of CTCF in breast cancer cells is associated with resistance to apoptosis. Cancer Res. (2005) 65(12):5112-5122.
   PubMed Web of Science ®Google Scholar
• BIANCHI L, CANTON C, BINI L et al.: Protein profile changes in the human breast cancer cell line MCF-7 in response to SEL1L gene induction. Proteomics (2005) 5(9):2433-2442.
   PubMed Web of Science ®Google Scholar
• CICEK M, SAMANT RS, KINTER M, WELCH DR, CASEY G: Identification of metastasis-associated proteins through protein analysis of metastatic MDA-MB-435 and metastasis-suppressed BRMS1 transfected-MDA-MB-435 cells. Clin. Exp. Metastasis (2004) 21(2):149-157.
   PubMed Web of Science ®Google Scholar
• POLISENO L, BIANCHI L, CITTI L et al.: Bcl2-low-expressing MCF7 cells undergo necrosis rather than apoptosis upon staurosporine treatment. Biochem. J. (2004) 379(Pt 3):823-832.
   PubMed Web of Science ®Google Scholar
• WHITE SL, GHARBI S, BERTANI MF et al.: Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression. Br. J. Cancer (2004) 90(1):173-181.
   PubMed Web of Science ®Google Scholar
• ZHANG DH, TAI LK, WONG LL, SETHI SK, KOAY ES: Proteomics of breast cancer: enhanced expression of cytokeratin19 in human epidermal growth factor receptor Type 2 positive breast tumors. Proteomics (2005) 5(7):1797-1805.
   PubMed Web of Science ®Google Scholar
• ZHANG D, TAI LK, WONG LL et al.: Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol. Cell. Proteomics (2005) 4(11):1686-1696.
   PubMed Web of Science ®Google Scholar
• BOSE R, MOLINA H, PATTERSON AS et al.: Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc. Natl. Acad. Sci. USA (2006) 103(26):9773-9778.
   Google Scholar
• WISEMAN BS, WERB Z: Stromal effects on mammary gland development and breast cancer. Science (2002) 296(5570):1046-1049.
   PubMed Web of Science ®Google Scholar
• CELIS JE, MOREIRA JM, CABEZON T et al.: Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients: toward dissecting the molecular circuitry of epithelial-adipocyte stromal cell interactions. Mol. Cell. Proteomics (2005) 4(4):492-522.
   PubMed Web of Science ®Google Scholar
• ZUCCHI I, DULBECCO R: Proteomic dissection of dome formation in a mammary cell line. J. Mammary Gland Biol. Neoplasia (2002) 7(4):373-384.
   PubMed Web of Science ®Google Scholar
• FERNANDEZ MADRID F: Autoantibodies in breast cancer sera: candidate biomarkers and reporters of tumorigenesis. Cancer Lett. (2005) 230(2):187-198.
   PubMed Web of Science ®Google Scholar
• ADAM PJ, BOYD R, TYSON KL et al.: Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J. Biol. Chem. (2003) 278(8):6482-6489.
   PubMed Web of Science ®Google Scholar
• BISSELL MJ, RADISKY D: Putting tumours in context. Nat. Rev. Cancer (2001) 1(1):46-54.
   Google Scholar
• FONTANA S, PUCCI-MINAFRA I, BECCHI M, FREYRIA AM, MINAFRA S: Effect of collagen substrates on proteomic modulation of breast cancer cells. Proteomics (2004) 4(3):849-860.
   PubMed Web of Science ®Google Scholar
• RIFAI N, GILLETTE MA, CARR SA: Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. (2006) 24(8):971-983.
   PubMed Web of Science ®Google Scholar
• HARTWELL L, MANKOFF D, PAULOVICH A, RAMSEY S, SWISHER E: Cancer biomarkers: a systems approach. Nat. Biotechnol. (2006) 24(8):905-908.
   PubMed Web of Science ®Google Scholar
• TAYLOR CF, HERMJAKOB H, JULIAN RK JR et al.: The work of the Human Proteome Organisation’s Proteomics Standards Initiative (HUPO PSI). Omics (2006) 10(2):145-151.
   PubMed Web of Science ®Google Scholar
• MCGEE S, O’CONNOR DP, GALLAGHER WM: Functional interrogation of breast cancer: from models to drugs. Expert Opin. Drug Discov. (2006) 1(6):569-584.
   PubMed Web of Science ®Google Scholar
• CELIS JE, GROMOV P, GROMOVA I et al.: Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research. Mol. Cell. Proteomics (2003) 2(6):369-377.
   PubMed Web of Science ®Google Scholar
• PETRICOIN EF, ZOON KC, KOHN EC, BARRETT JC, LIOTTA LA: Clinical proteomics: translating benchside promise into bedside reality. Nat. Rev. Drug Discov. (2002) 1(9):683-695.
   PubMed Web of Science ®Google Scholar
• VITZTHUM F, BEHRENS F, ANDERSON NL, SHAW JH: Proteomics: from basic research to diagnostic application. A review of requirements & needs. J. Proteome Res. (2005) 4(4):1086-1097.
   PubMed Web of Science ®Google Scholar
• ADAM PJ, BERRY J, LOADER JA et al.: 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(11):826-835.
   Google Scholar
• 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(5):791-796.
   PubMed Web of Science ®Google Scholar
• ROBERTS K, BHATIA K, STANTON P, LORD R: Proteomic analysis of selected prognostic factors of breast cancer. Proteomics (2004) 4(3):784-792.
   PubMed Web of Science ®Google Scholar
• SANDHU C, CONNOR M, KISLINGER T, SLINGERLAND J, EMILI A: Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells. J. Proteome Res. (2005) 4(3):674-689.
   PubMed Web of Science ®Google Scholar
• JESSANI N, LIU Y, HUMPHREY M, CRAVATT BF: Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl. Acad. Sci. USA (2002) 99(16):10335-10340.
   Google Scholar
• SPEERS AE, CRAVATT BF: Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. (2004) 11(4):535-546.
   PubMed Web of Science ®Google Scholar