Search for breast cancer biomarkers in fractionated serum samples by protein profiling with SELDI-TOF MS

Journal of Clinical Laboratory Analysis

Volumn 26, Issue 1, 2012, Pages 1-9

  Opstal van Winden, Annemieke W J ^a,b   Beijnen, Jos H ^b,c   Loof, Arnoud ^d   van Heerde, Waander L ^d   Vermeulen, Roel ^a,e   Peeters, Petra H M ^a,f   van Gils, Carla H ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b NETHERLANDS CANCER INSTITUTE   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e UTRECHT UNIVERSITY   (Netherlands)

^f IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Biomarker; Breast cancer; Fractionation; Proteomics; SELDI TOF MS

Indexed keywords

APOLIPOPROTEIN A1; APOLIPOPROTEIN A2; APOLIPOPROTEIN C2; APOLIPOPROTEIN C3; HEMOGLOBIN BETA CHAIN; TUMOR MARKER;

ADULT; ARTICLE; BREAST CANCER; CANCER INCIDENCE; CONTROLLED STUDY; FEMALE; HUMAN; MAJOR CLINICAL STUDY; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; BLOOD; BREAST TUMOR; CASE CONTROL STUDY; MASS SPECTROMETRY; MIDDLE AGED; PILOT STUDY; PROTEIN MICROARRAY; RETROSPECTIVE STUDY; STATISTICAL MODEL;

BREAST NEOPLASMS; CASE-CONTROL STUDIES; FEMALE; HUMANS; LOGISTIC MODELS; MIDDLE AGED; PILOT PROJECTS; PROTEIN ARRAY ANALYSIS; RETROSPECTIVE STUDIES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84868569226     PISSN: 08878013     EISSN: 10982825     Source Type: Journal    
DOI: 10.1002/jcla.20492     Document Type: Article

References (37)

1. Belluco C, Petricoin EF, Mammano E, et al. Serum proteomic analysis identifies a highly sensitive and specific discriminatory pattern in stage 1 breast cancer. Ann Surg Oncol 2007;14:2470-2476.
2. 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;115:783-789.
3. 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;48:1296-1304.
4. van Winden AW, Gast MC, Beijnen JH, et al. Validation of previously identified serum biomarkers for breast cancer with SELDITOF MS: A case control study. BMC Med Genomics 2009;2:4.
5. Li J, Orlandi R, White CN, et al. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin Chem 2005;51:2229-2235.
6. Mathelin C, Cromer A, Wendling C, Tomasetto C, Rio MC. Serum biomarkers for detection of breast cancers: A prospective study. Breast Cancer Res Treat 2006;96:83-90.
7. Song J, Patel M, Rosenzweig CN, et al. Quantification of fragments of human serum inter-alpha-trypsin inhibitor heavy chain 4 by a surface-enhanced laser desorption/ionization-based immunoassay. Clin Chem 2006;52:1045-1053.
8. 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;14:250-255.
9. Vlahou A, Laronga C, Wilson L, et al. A novel approach toward development of a rapid blood test for breast cancer. Clin Breast Cancer 2003;4:203-209.
10. Engwegen JY, Helgason HH, Cats A, et al. Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry. World J Gastroenterol 2006;12:1536-1544.
11. Engwegen JY, Depla AC, Smits ME, et al. Detection of colorectal cancer by serum and tissue protein profiling: A prospective study in a population at risk. Biomark Insights 2008;3:375-385.
12. Engwegen JY,Mehra N, Haanen JB, Schellens JH, Voest EE, Beijnen JH. Identification of two new serum protein profiles for renal cell carcinoma. Oncol Rep 2009;22:401-408.
13. Gast MC, Schellens JH, Beijnen JH. Clinical proteomics in breast cancer: A review. Breast Cancer Res Treat 2009;116:17-29.
14. Hoffman SA, Joo WA, Echan LA, Speicher DW. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2007;849:43-52.
15. Anderson NL, Anderson NG. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 2002;1:845-867.
16. Faca V, Pitteri SJ, Newcomb L, et al. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 2007;6:3558-3565.
17. Vermeulen R, Lan Q, Zhang L, et al. Decreased levels of CXCchemokines in serum of benzene-exposed workers identified by array-based proteomics. Proc Natl Acad Sci USA 2005;102:17041-17046.
18. Restuccia U, Boschetti E, Fasoli E, et al. pI-based fractionation of serum proteomes versus anion exchange after enhancement of low-abundance proteins by means of peptide libraries. J Proteomics 2009;72:1061-1070.
19. Sahab ZJ, Iczkowski KA, Sang QX. Anion exchange fractionation of serum proteins versus albumin elimination. Anal Biochem 2007;368:24-32.
20. Yocum AK, Yu K, Oe T, Blair IA. Effect of immunoaffinity depletion of human serum during proteomic investigations. J Proteome Res 2005;4:1722-1731.
21. Karsan A, Eigl BJ, Flibotte S, et al. Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin Chem 2005;51:1525-1528.
22. Pelikan R, Bigbee WL, Malehorn D, Lyons-Weiler J, Hauskrecht M. Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models. Bioinformatics 2007;23:3065-3072.
23. 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;3:322-331.
24. Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 1995;57:289-300.
25. Timms JF, Arslan-Low E, Gentry-Maharaj A, et al. Preanalytic influence of sample handling on SELDI-TOF serum protein profiles. Clin Chem 2007;53:645-656.
26. Trak-Smayra V, Dargere D, Noun R, et al. Serum proteomic profiling of obese patients: Correlationwith liver pathology and evolution after bariatric surgery. Gut 2009;58:825-832.
27. Kozak KR, Su F, Whitelegge JP, Faull K, Reddy S, Farias-Eisner R. Characterization of serum biomarkers for detection of early stage ovarian cancer. Proteomics 2005;5:4589-4596.
28. Sundsten T, Zethelius B, Berne C, Bergsten P. Plasma proteome changes in subjects with Type 2 diabetes mellitus with a low or high early insulin response. Clin Sci (Lond) 2008;114:499-507.
29. Woong-Shick A, Sung-Pil P, Su-Mi B, et al. Identification of hemoglobin-alpha and -beta subunits as potential serum biomarkers for the diagnosis and prognosis of ovarian cancer. Cancer Sci 2005;96:197-201.
30. Tammen H, Mohring T, Kellmann M, Pich A, Kreipe HH, Hess R. Mass spectrometric phenotyping of Val34Leu polymorphism of blood coagulation factor XIII by differential peptide display. Clin Chem 2004;50:545-551.
31. Jiang WG, Ablin R, Douglas-Jones A, Mansel RE. Expression of transglutaminases in human breast cancer and their possible clinical significance. Oncol Rep 2003;10:2039-2044.
32. Villanueva J, Shaffer DR, Philip J, et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006;116:271-284.
33. 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.
34. Rollin D, Whistler T, Vernon SD. Laboratory methods to improve SELDI peak detection and quantitation. Proteome Sci 2007;5:9.
35. Harezlak J, Wang M, Christiani D, Lin X. Quantitative qualityassessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments. Bioinformatics 2007;23:2441-2448.
36. Solassol J, Marin P, Demettre E, et al. Proteomic detection of prostate-specific antigen using a serum fractionation procedure: Potential implication for new low-abundance cancer biomarkers detection. Anal Biochem 2005;338:26-31.
37. Gast MC, van Gils CH, Wessels LF, et al. Influence of sample storage duration on serum protein profiles assessed by surfaceenhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS). Clin Chem Lab Med 2009;47:694-705.