Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Clinical Chemistry and Laboratory Medicine (CCLM)

Published in Association with the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM)

Editor-in-Chief: Plebani, Mario

Ed. by Gillery, Philippe / Lackner, Karl J. / Lippi, Giuseppe / Melichar, Bohuslav / Payne, Deborah A. / Schlattmann, Peter / Tate, Jillian R.

12 Issues per year


IMPACT FACTOR 2016: 3.432

CiteScore 2016: 2.21

SCImago Journal Rank (SJR) 2016: 1.000
Source Normalized Impact per Paper (SNIP) 2016: 1.112

Online
ISSN
1437-4331
See all formats and pricing
More options …
Volume 43, Issue 12 (Dec 2005)

Issues

SELDI-TOF-MS proteomics of breast cancer

Charlotte H. Clarke / Julie A. Buckley
  • Department of Radiology, Palo Alto Medical Foundation, Palo Alto, CA, United States of America
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Eric T. Fung
Published Online: 2005-11-28 | DOI: https://doi.org/10.1515/CCLM.2005.225

Abstract

The detection, diagnosis, and management of breast cancer rely on an integrated approach using clinical history, physical examination, imaging, and histopathology. The discovery and validation of novel biomarkers will aid the physician in more effectively achieving this integration. This review discusses efforts in surface-enhanced laser desorption/ionization (SELDI)-based proteomics to address various clinical questions surrounding breast cancer, including diagnosis, monitoring, and stratification for treatment. Emphasis is placed on examining how study design and execution influence the discovery and validation process, which is critical to the proper development of potential clinical tests.

Keywords: biomarkers; breast cancer; diagnostics; proteomics; surface enhanced laser desorption/ionization (SELDI)

References

  • 1.

    Jemal A, Murray T, Ward E, Samuels A, Tiwari RC, Ghafoor A, et al. Cancer statistics, 2005. CA Cancer J Clin 2005; 55:10–30.CrossrefGoogle Scholar

  • 2.

    Antman K, Shea S. Screening mammography under age 50. J Am Med Assoc 1999; 281:1470–2.Google Scholar

  • 3.

    Lumachi F, Basso SM. Serum tumor markers in patients with breast cancer. Expert Rev Anticancer Ther 2004; 4:921–31.CrossrefGoogle Scholar

  • 4.

    Esteva FJ, Hortobagyi GN. Prognostic molecular markers in early breast cancer. Breast Cancer Res 2004; 6:109–18.CrossrefGoogle Scholar

  • 5.

    Jacquemier J, Ginestier C, Rougemont J, Bardou VJ, Charafe-Jauffret E, Geneix J, et al. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res 2005; 65:767–79.Google Scholar

  • 6.

    Somiari RI, Somiari S, Russell S, Shriver CD. Proteomics of breast carcinoma. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815:215–25.Google Scholar

  • 7.

    Celis JE, Gromov P, Cabezon T, Moreira JM, Ambartsumian N, Sandelin K, 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; 3:327–44.CrossrefGoogle Scholar

  • 8.

    Stein RC, Zvelebil MJ. The application of 2D gel-based proteomics methods to the study of breast cancer. J Mammary Gland Biol Neoplasia 2002; 7:385–93.CrossrefGoogle Scholar

  • 9.

    Hathout Y, Gehrmann ML, Chertov A, Fenselau C. Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett 2004; 210:245–53.Google Scholar

  • 10.

    Yates JR III. Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 2004; 33:297–316.CrossrefGoogle Scholar

  • 11.

    Rodland KD. Proteomics and cancer diagnosis: the potential of mass spectrometry. Clin Biochem 2004; 37:579–83.CrossrefGoogle Scholar

  • 12.

    Veenstra TD, Prieto DA, Conrads TP. Proteomic patterns for early cancer detection. Drug Discov Today 2004; 9:889–97.CrossrefGoogle Scholar

  • 13.

    Espina V, Dettloff KA, Cowherd S, Petricoin EF III, Liotta LA. Use of proteomic analysis to monitor responses to biological therapies. Expert Opin Biol Ther 2004; 4:83–93.CrossrefGoogle Scholar

  • 14.

    Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom Rev 2004; 23:34–44.CrossrefGoogle Scholar

  • 15.

    Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun 2002; 292:587–92.Google Scholar

  • 16.

    Oehr P. Proteomics as a tool for detection of nuclear matrix proteins and new biomarkers for screening of early tumors stage. Anticancer Res 2003; 23:805–12.Google Scholar

  • 17.

    Fung ET, Enderwick C. ProteinChip clinical proteomics: computational challenges and solutions. Biotechniques 2002; 32(Suppl):34–41.Google Scholar

  • 18.

    Kearney P, Thibault P. Bioinformatics meets proteomics – bridging the gap between mass spectrometry data analysis and cell biology. J Bioinform Comput Biol 2003; 1:183–200.CrossrefGoogle Scholar

  • 19.

    White CN, Chan DW, Zhang Z. Bioinformatics strategies for proteomic profiling. Clin Biochem 2004; 37:636–41.CrossrefGoogle Scholar

  • 20.

    Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling – a young technology begins to mature. Nat Biotechnol 2005; 23:291–2.CrossrefGoogle Scholar

  • 21.

    Hu J, Coombes KR, Morris JS, Baggerly KA. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic 2005; 3:322–31.Google Scholar

  • 22.

    White CN, Zhang Z, Chan DW. Quality control for SELDI analysis. Clin Chem Lab Med 2005; 43:125–6.Google Scholar

  • 23.

    Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 2004; 96:353–6.CrossrefGoogle Scholar

  • 24.

    Zhang Z, Bast RC Jr, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004; 64:5882–90.CrossrefGoogle Scholar

  • 25.

    Semmes OJ, Feng Z, Adam BL, Banez LL, Bigbee WL, Campos D, et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin Chem 2005; 51:102–12.CrossrefGoogle Scholar

  • 26.

    Ransohoff DF. Rules of evidence for cancer molecular-marker discovery and validation. Nat Rev Cancer 2004; 4:309–14.CrossrefGoogle Scholar

  • 27.

    Vlahou A, Laronga C, Wilson L, Gregory B, Fournier K, McGaughey D, et al. A novel approach toward development of a rapid blood test for breast cancer. Clin Breast Cancer 2003; 4:203–9.CrossrefGoogle Scholar

  • 28.

    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; 48:1296–304.Google Scholar

  • 29.

    Donegan WL. Evaluation of a palpable breast mass. N Engl J Med 1992; 327:937–42.Google Scholar

  • 30.

    Hu Y, Zhang SZ, Yu JK, Liu J, Zheng S, Hu X. [Diagnostic application of serum protein pattern and artificial neural network software in breast cancer.]. Ai Zheng 2005; 24:67–71.Google Scholar

  • 31.

    Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, et al. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer 2004; 100:1814–22.CrossrefGoogle Scholar

  • 32.

    Caputo E, Lombardi ML, Luongo V, Moharram R, Tornatore P, Pirozzi G, et al. Peptide profiling in epithelial tumor plasma by the emerging proteomic techniques. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 819:59–66.Google Scholar

  • 33.

    Fung ET, Yip TT, Lomas L, Wang Z, Yip C, Meng XY, et al. Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int J Cancer 2005; 115:783–9.CrossrefGoogle Scholar

  • 34.

    King MC, Marks JH, Mandell JB. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science 2003; 302:643–6.Google Scholar

  • 35.

    Laronga C, Becker S, Watson P, Gregory B, Cazares L, Lynch H, et al. SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers. Dis Markers 2003; 19:229–38.CrossrefGoogle Scholar

  • 36.

    Becker S, Cazares LH, Watson P, Lynch H, Semmes OJ, Drake RR, et al. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer. Ann Surg Oncol 2004; 11:907–14.Google Scholar

  • 37.

    Heike Y, Hosokawa M, Osumi S, Fujii D, Aogi K, Takigawa N, et al. Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI Protein-Chip system. Anticancer Res 2005; 25:1197–203.Google Scholar

  • 38.

    Khan SA. The role of ductal lavage in the management of women at high risk for breast carcinoma. Curr Treat Options Oncol 2004; 5:145–51.Google Scholar

  • 39.

    Petricoin EE, Paweletz CP, Liotta LA. Clinical applications of proteomics: proteomic pattern diagnostics. J Mammary Gland Biol Neoplasia 2002; 7:433–40.CrossrefGoogle Scholar

  • 40.

    Paweletz CP, Trock B, Pennanen M, Tsangaris T, Magnant C, Liotta LA, 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; 17:301–7.CrossrefGoogle Scholar

  • 41.

    Kuerer HM, Coombes KR, Chen JN, Xiao L, Clarke C, Fritsche H, et al. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery 2004; 136:1061–9.Google Scholar

  • 42.

    Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, 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; 89:149–57.CrossrefGoogle Scholar

  • 43.

    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; 86:1440–3.CrossrefGoogle Scholar

  • 44.

    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; 114:791–6.CrossrefGoogle Scholar

  • 45.

    Mendrinos S, Nolen JD, Styblo T, Carlson G, Pohl J, Lewis M, et al. Cytologic findings and protein expression profiles associated with ductal carcinoma of the breast in ductal lavage specimens using surface-enhanced laser desorption and ionization-time of flight mass spectrometry. Cancer 2005; 105:178–83.CrossrefGoogle Scholar

  • 46.

    Fowler LJ, Lovell MO, Izbicka E. Fine-needle aspiration in PreservCyt: a novel and reproducible method for possible ancillary proteomic pattern expression of breast neoplasms by SELDI-TOF. Mod Pathol 2004; 17:1012–20.CrossrefGoogle Scholar

  • 47.

    Coombes KR, Fritsche HA Jr, Clarke C, Chen JN, Baggerly KA, Morris JS, 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; 49:1615–23.CrossrefGoogle Scholar

  • 48.

    Mian S, Ball G, Hornbuckle J, Holding F, Carmichael J, Ellis I, 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; 3:1725–37.Google Scholar

  • 49.

    Carter D, Douglass JF, Cornellison CD, Retter MW, Johnson JC, Bennington AA, et al. Purification and characterization of the mammaglobin/lipophilin B complex, a promising diagnostic marker for breast cancer. Biochemistry 2002; 41:6714–22.CrossrefGoogle Scholar

  • 50.

    Euhus DM. Understanding mathematical models for breast cancer risk assessment and counseling. Breast J 2001; 7:224–32.CrossrefGoogle Scholar

  • 51.

    Kriege M, Brekelmans CT, Boetes C, Besnard PE, Zonderland HM, Obdeijn IM, et al. Efficacy of MRI and mammography for breast-cancer screening in women with a familial or genetic predisposition. N Engl J Med 2004; 351:427–37.Google Scholar

  • 52.

    van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347:1999–2009.Google Scholar

  • 53.

    Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004; 351:2817–26.Google Scholar

  • 54.

    Celis JE, Gromov P, Gromova I, Moreira JM, Cabezon T, Ambartsumian N, et al. Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research. Mol Cell Proteomics 2003; 2:369–77.Google Scholar

  • 55.

    Celis JE, Moreira JM, Gromova I, Cabezon T, Ralfkiaer U, Guldberg P, et al. Towards discovery-driven translational research in breast cancer. FEBS J 2005; 272:2–15.Google Scholar

About the article

Corresponding author: Eric T. Fung, Ciphergen Biosystems, Inc., Diagnostics Division, 6611 Dumbarton Circle, Fremont, CA 94555, USA Phone: +1-510-505-2242, Fax: +1-510-505-2101,


Received: 2005-06-29

Accepted: 2005-10-10

Published Online: 2005-11-28

Published in Print: 2005-12-01


Citation Information: Clinical Chemistry and Laboratory Medicine (CCLM), ISSN (Online) 1437-4331, ISSN (Print) 1434-6621, DOI: https://doi.org/10.1515/CCLM.2005.225.

Export Citation

©2005 by Walter de Gruyter Berlin New York. Copyright Clearance Center

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Wei Li, Jian-Fang Li, Ying Qu, Xue-Hua Chen, Jian-Min Qin, Qin-Long Gu, Min Yan, Zheng-Gang Zhu, and Bing-Ya Liu
World Journal of Gastroenterology, 2008, Volume 14, Number 37, Page 5657
[2]
CHIBO LIU, CHUNQIN PAN, and YONG LIANG
Experimental and Therapeutic Medicine, 2012, Volume 3, Number 6, Page 1005
[3]
François Bertucci, Daniel Birnbaum, and Anthony Goncalves
Molecular & Cellular Proteomics, 2006, Volume 5, Number 10, Page 1772
[4]
Nilofer S. Azad, Nabila Rasool, Christina M. Annunziata, Lori Minasian, Gordon Whiteley, and Elise C. Kohn
Molecular & Cellular Proteomics, 2006, Volume 5, Number 10, Page 1819
[5]
Rocco Savino, Sergio Paduano, Mariaimmacolata Preianò, and Rosa Terracciano
International Journal of Molecular Sciences, 2012, Volume 13, Number 12, Page 13926
[6]
[7]
Johana A. Luna Coronell, Parvez Syed, Khulan Sergelen, István Gyurján, and Andreas Weinhäusel
Journal of Proteomics, 2012, Volume 76, Page 102
[8]
Chibo Liu
Pathology & Oncology Research, 2012, Volume 18, Number 2, Page 117
[9]
Luc Guerrier, Benoit D'Autreaux, Christo Atanassov, Ghalia Khoder, and Egisto Boschetti
Journal of Proteomics, 2008, Volume 71, Number 3, Page 368
[10]
Stéphane Roche, Laurent Tiers, Monique Provansal, Martial Seveno, Marie-Thérèse Piva, Patrick Jouin, and Sylvain Lehmann
Journal of Proteomics, 2009, Volume 72, Number 6, Page 945
[11]
Ciara A. McManus, Marlene L. Rose, and Michael J. Dunn
Transplantation Reviews, 2006, Volume 20, Number 4, Page 195
[12]
Feng Ge, Li-Jun Bi, Sheng-Ce Tao, Xu-dong Xu, Zhi-Ping Zhang, Kaio Kitazato, and Xian-En Zhang
PROTEOMICS - Clinical Applications, 2011, Volume 5, Number 1-2, Page 30
[13]
Joseph S.K. Au, William C.S. Cho, Tai Tung Yip, Christine Yip, Hailong Zhu, Wallace W.F. Leung, Philip Y.B. Tsui, Davy L.P. Kwok, Simon S.M. Kwan, Wai Wai Cheng, Lawrence C.H. Tzang, Mengsu Yang, and Stephen C.K. Law
Biomedicine & Pharmacotherapy, 2007, Volume 61, Number 9, Page 570
[14]
Emanuela Monari, Christian Casali, Aurora Cuoghi, Jessica Nesci, Elisa Bellei, Stefania Bergamini, Luca I Fantoni, Pamela Natali, Uliano Morandi, and Aldo Tomasi
Proteome Science, 2011, Volume 9, Number 1, Page 55
[15]
Huey-Miin Hsueh, Hsun-chih Kuo, and Chen-An Tsai
Journal of Biopharmaceutical Statistics, 2008, Volume 18, Number 5, Page 869
[16]
Chunwei Li, Dianliang Zhang, Jian Zhang, Fengbo Sun, and Lei Mi
The Chinese-German Journal of Clinical Oncology, 2011, Volume 10, Number 5, Page 261
[17]
A. Baillet, C. Trocme, S. Berthier, M. Arlotto, L. Grange, J. Chenau, S. Quetant, M. Seve, F. Berger, R. Juvin, F. Morel, and P. Gaudin
Rheumatology, 2010, Volume 49, Number 4, Page 671
[18]
Sergio Ciordia, Vivian de los Ríos, and Juan-Pablo Albar
Clinical and Translational Oncology, 2006, Volume 8, Number 8, Page 566
[19]
Marta Lomnytska and Serhiy Souchelnytskyi
PROTEOMICS – CLINICAL APPLICATIONS, 2007, Volume 1, Number 9, Page 1090
[20]
[21]
Gernot P. Tilz, Marco Wiltgen, Ulrike Demel, Christian Faschinger, Hannes Schmidinger, and Albin Hermetter
Wiener Medizinische Wochenschrift, 2007, Volume 157, Number 5-6, Page 122
[22]
Rania Bakry, Christian W. Huck, Muhammed Najam-ul-Haq, Matthias Rainer, and Günther K. Bonn
Journal of Separation Science, 2007, Volume 30, Number 2, Page 192
[23]
Giuseppe Grasso, Marco Fragai, Enrico Rizzarelli, Giuseppe Spoto, and Kwon Joo Yeo
Journal of Mass Spectrometry, 2006, Volume 41, Number 12, Page 1561
[24]
Estelle Peronnet, Laurence Becquart, Florence Poirier, Myriam Cubizolles, Geneviève Choquet-Kastylevsky, and Colette Jolivet-Reynaud
PROTEOMICS, 2006, Volume 6, Number 23, Page 6288
[25]
Moulay A. Alaoui-Jamali and Ying-jie Xu
Journal of Zhejiang University SCIENCE B, 2006, Volume 7, Number 6, Page 411

Comments (0)

Please log in or register to comment.
Log in