Targeted in-gel MRM: A hypothesis driven approach for colorectal cancer biomarker discovery in human feces

Journal of Proteome Research

Volumn 9, Issue 9, 2010, Pages 4346-4355

  Ang, Ching Seng ^a,b   Nice, Edouard C ^a,b,c  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (Sweden)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c MONASH UNIVERSITY   (Australia)

Author keywords

18O labeling; biomarkers; colorectal cancer; comparative proteomics; fecal proteomics; MRM

Indexed keywords

BIOLOGICAL MARKER; CALCYCLIN; CALGRANULIN A; CALGRANULIN B; CARCINOEMBRYONIC ANTIGEN; CATHEPSIN S; COLORECTAL CANCER ASSOCIATED PROTEIN; DIPEPTIDYL PEPTIDASE IV; FILAMIN A; FILAMIN C; HEMOGLOBIN; HEMOGLOBIN A; HEMOGLOBIN BETA CHAIN; L PLASTIN; LYSOSOME ASSOCIATED MEMBRANE GLYCOPROTEIN 2; MYELOPEROXIDASE; NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN; PROFILIN I; PROLACTIN INDUCIBLE PROTEIN; PROTOCADHERIN 24; SELENIUM BINDING PROTEIN; SUCRASE ISOMALTASE; UNCLASSIFIED DRUG;

ARTICLE; CLINICAL ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; FECES; HUMAN; HYPOTHESIS; MOLECULAR WEIGHT; MULTIPLE REACTION MONITORING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; SCREENING;

AMINO ACID SEQUENCE; COLORECTAL NEOPLASMS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FECES; FEMALE; HUMANS; ISOTOPE LABELING; LINEAR MODELS; MALE; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEINS; PROTEOME; REPRODUCIBILITY OF RESULTS; TUMOR MARKERS, BIOLOGICAL;

EID: 77956306460     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr100509e     Document Type: Article

References (61)

1. Jemal, A.; Siegel, R.; Ward, E.; Hao, Y.; Xu, J.; Murray, T.; Thun, M. J. Cancer statistics, 2008 CA. Cancer J. Clin. 2008, 58 (2) 71-96
2. Etzioni, R.; Urban, N.; Ramsey, S.; McIntosh, M.; Schwartz, S.; Reid, B.; Radich, J.; Anderson, G.; Hartwell, L. The case for early detection Nat. Rev. Cancer 2003, 3 (4) 243-52
3. Nakazato, M.; Yamano, H.; Matsushita, H.; Sato, K.; Fujita, K.; Yamanaka, Y.; Imai, Y. Immunologic fecal occult blood test for colorectal cancer screening Japan Med. Assoc. J. 2006, 49 (5) 203-207
4. Simpson, R. J.; Bernhard, O. K.; Greening, D. W.; Moritz, R. L. Proteomics-driven cancer biomarker discovery: looking to the future Curr. Opin. Chem. Biol. 2008, 12 (1) 72-7
5. 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 (3) 377-96
6. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat. Biotechnol. 1999, 17 (10) 994-9
7. Yao, X.; Freas, A.; Ramirez, J.; Demirev, P. A.; Fenselau, C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus Anal. Chem. 2001, 73 (13) 2836-42
8. Ross, P. L.; Huang, Y. N.; Marchese, J. N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D. J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3 (12) 1154-69
9. Ang, C. S.; Veith, P. D.; Dashper, S. G.; Reynolds, E. C. Application of 16O/18O reverse proteolytic labeling to determine the effect of biofilm culture on the cell envelope proteome of Porphyromonas gingivalis W50 Proteomics 2008, 8 (8) 1645-60
10. Pang, J. X.; Ginanni, N.; Dongre, A. R.; Hefta, S. A.; Opitek, G. J. Biomarker discovery in urine by proteomics J. Proteome Res. 2002, 1 (2) 161-9
11. Lehmann, U.; Wienkoop, S.; Tschoep, H.; Weckwerth, W. If the antibody fails - a mass western approach Plant J. 2008, 55 (6) 1039-46
12. Kuzyk, M. A.; Smith, D.; Yang, J.; Cross, T. J.; Jackson, A. M.; Hardie, D. B.; Anderson, N. L.; Borchers, C. H. MRM-based, multiplexed, absolute quantitation of 45 proteins in human plasma Mol. Cell. Proteomics 2009, 8 (8) 1860-77
13. Zolg, J. W.; Langen, H. How industry is approaching the search for new diagnostic markers and biomarkers Mol. Cell. Proteomics 2004, 3 (4) 345-54
14. Faca, V.; Krasnoselsky, A.; Hanash, S. Innovative proteomic approaches for cancer biomarker discovery BioTechniques 2007, 43 (3) 281-3, 285 279
15. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Mol. Cell. Proteomics 2006, 5 (4) 573-88
16. Picotti, P.; Rinner, O.; Stallmach, R.; Dautel, F.; Farrah, T.; Domon, B.; Wenschuh, H.; Aebersold, R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nat. Methods 2010, 7 (1) 43-6
17. Hung, K. E.; Kho, A. T.; Sarracino, D.; Richard, L. G.; Krastins, B.; Forrester, S.; Haab, B. B.; Kohane, I. S.; Kucherlapati, R. Mass spectrometry-based study of the plasma proteome in a mouse intestinal tumor model J. Proteome Res. 2006, 5 (8) 1866-78
18. Osborn, N. K.; Ahlquist, D. A. Stool screening for colorectal cancer: molecular approaches Gastroenterology 2005, 128 (1) 192-206
19. Kim, Y.; Lee, S.; Park, S.; Jeon, H.; Lee, W.; Kim, J. K.; Cho, M.; Kim, M.; Lim, J.; Kang, C. S.; Han, K. Gastrointestinal tract cancer screening using fecal carcinoembryonic antigen Ann. Clin. Lab. Sci. 2003, 33 (1) 32-8
20. Ramsoekh, D.; van Leerdam, M. E.; van Ballegooijen, M.; Habbema, J. D.; Kuipers, E. J. Population screening for colorectal cancer: faeces, endoscopes or X-rays Cell. Oncol. 2007, 29 (3) 185-94
21. Lotze, M. T.; Wang, E.; Marincola, F. M.; Hanna, N.; Bugelski, P. J.; Burns, C. A.; Coukos, G.; Damle, N.; Godfrey, T. E.; Howell, W. M.; Panelli, M. C.; Perricone, M. A.; Petricoin, E. F.; Sauter, G.; Scheibenbogen, C.; Shivers, S. C.; Taylor, D. L.; Weinstein, J. N.; Whiteside, T. L. Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health J. Immunother. 2005, 28 (2) 79-119
22. Verberkmoes, N. C.; Russell, A. L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarson, J.; Lefsrud, M. G.; Apajalahti, J.; Tysk, C.; Hettich, R. L.; Jansson, J. K. Shotgun metaproteomics of the human distal gut microbiota ISME J. 2009, 3 (2) 179-89
23. Ang, C. S.; Rothacker, J.; Patsiouras, H.; Burgess, A. W.; Nice, E. C. Murine fecal proteomics: A model system for the detection of potential biomarkers for colorectal cancer J. Chromatogr. A 2010, 1217 (19) 3330-40
24. Simpson, R. J.; Connolly, L. M.; Eddes, J. S.; Pereira, J. J.; Moritz, R. L.; Reid, G. E. Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database Electrophoresis 2000, 21 (9) 1707-32
25. Craig, R.; Cortens, J. P.; Beavis, R. C. Open source system for analyzing, validating, and storing protein identification data J. Proteome Res. 2004, 3 (6) 1234-42
26. Desiere, F.; Deutsch, E. W.; King, N. L.; Nesvizhskii, A. I.; Mallick, P.; Eng, J.; Chen, S.; Eddes, J.; Loevenich, S. N.; Aebersold, R. The PeptideAtlas project Nucleic Acids Res. 2006, 34 (Database issue) D655-8
27. Mead, J. A.; Bianco, L.; Ottone, V.; Barton, C.; Kay, R. G.; Lilley, K. S.; Bond, N. J.; Bessant, C. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions Mol. Cell. Proteomics 2009, 8 (4) 696-705
28. Mallick, P.; Schirle, M.; Chen, S. S.; Flory, M. R.; Lee, H.; Martin, D.; Ranish, J.; Raught, B.; Schmitt, R.; Werner, T.; Kuster, B.; Aebersold, R. Computational prediction of proteotypic peptides for quantitative proteomics Nat. Biotechnol. 2007, 25 (1) 125-31
29. Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76 (14) 3908-22
30. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and localized protons: a framework for understanding peptide dissociation J. Mass Spectrom. 2000, 35 (12) 1399-406
31. Kapp, E. A.; Schutz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O'Hair, R. A.; Speed, T. P.; Simpson, R. J. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation Anal. Chem. 2003, 75 (22) 6251-64
32. Kirkpatrick, D. S.; Gerber, S. A.; Gygi, S. P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications Methods 2005, 35 (3) 265-73
33. Gupta, M. K.; Jung, J. W.; Uhm, S. J.; Lee, H.; Lee, H. T.; Kim, K. P. Combining selected reaction monitoring with discovery proteomics in limited biological samples Proteomics 2009, 9 (21) 4834-6
34. Levi, Z.; Rozen, P.; Hazazi, R.; Vilkin, A.; Waked, A.; Maoz, E.; Birkenfeld, S.; Leshno, M.; Niv, Y. A quantitative immunochemical fecal occult blood test for colorectal neoplasia Ann. Intern. Med. 2007, 146 (4) 244-55
35. Karl, J.; Wild, N.; Tacke, M.; Andres, H.; Garczarek, U.; Rollinger, W.; Zolg, W. Improved diagnosis of colorectal cancer using a combination of fecal occult blood and novel fecal protein markers Clin. Gastroenterol. Hepatol. 2008, 6 (10) 1122-8
36. Roseth, A. G.; Fagerhol, M. K.; Aadland, E.; Schjonsby, H. Assessment of the neutrophil dominating protein calprotectin in feces. A methodologic study Scand. J. Gastroenterol. 1992, 27 (9) 793-8
37. Eckburg, P. B.; Bik, E. M.; Bernstein, C. N.; Purdom, E.; Dethlefsen, L.; Sargent, M.; Gill, S. R.; Nelson, K. E.; Relman, D. A. Diversity of the human intestinal microbial flora Science 2005, 308 (5728) 1635-8
38. Saiki, T. Myeloperoxidase concentrations in the stool as a new parameter of inflammatory bowel disease Kurume Med. J. 1998, 45 (1) 69-73
39. Itzkowitz, S. H.; Yio, X.; Inflammation and cancer IV Am. J. Physiol. Gastrointest. Liver Physiol. 2004, 287 (1) G7-17
40. Klaile, E.; Muller, M. M.; Kannicht, C.; Singer, B. B.; Lucka, L. CEACAM1 functionally interacts with filamin A and exerts a dual role in the regulation of cell migration J. Cell Sci. 2005, 118 (Pt 23) 5513-24
41. Foran, E.; McWilliam, P.; Kelleher, D.; Croke, D. T.; Long, A. The leukocyte protein L-plastin induces proliferation, invasion and loss of E-cadherin expression in colon cancer cells Int. J. Cancer 2006, 118 (8) 2098-104
42. Broedel, O.; Krause, E.; Stephanowitz, H.; Schuemann, M.; Eravci, M.; Weist, S.; Brunkau, C.; Wittke, J.; Eravci, S.; Baumgartner, A. In-Gel 18O labeling for improved identification of proteins from 2-DE Gel spots in comparative proteomic experiments J. Proteome Res. 2009, 8 (7) 3771-7
43. Baron, A. T.; Lafky, J. M.; Suman, V. J.; Hillman, D. W.; Buenafe, M. C.; Boardman, C. H.; Podratz, K. C.; Perez, E. A.; Maihle, N. J. A preliminary study of serum concentrations of soluble epidermal growth factor receptor (sErbB1), gonadotropins, and steroid hormones in healthy men and women Cancer Epidemiol. Biomarkers Prev. 2001, 10 (11) 1175-85
44. Dooley, K. C. Tandem mass spectrometry in the clinical chemistry laboratory Clin. Biochem. 2003, 36 (6) 471-81
45. Streit, F.; Armstrong, V. W.; Oellerich, M. Rapid liquid chromatography-tandem mass spectrometry routine method for simultaneous determination of sirolimus, everolimus, tacrolimus, and cyclosporin A in whole blood Clin. Chem. 2002, 48 (6 Pt 1) 955-8
46. Jaffe, J. D.; Keshishian, H.; Chang, B.; Addona, T. A.; Gillette, M. A.; Carr, S. A. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification Mol. Cell. Proteomics 2008, 7 (10) 1952-62
47. Han, B.; Higgs, R. E. Proteomics: from hypothesis to quantitative assay on a single platform. Guidelines for developing MRM assays using ion trap mass spectrometers Brief Funct. Genomic Proteomic 2008, 7 (5) 340-54
48. Poullis, A.; Foster, R.; Northfield, T. C.; Mendall, M. A. Review article: faecal markers in the assessment of activity in inflammatory bowel disease Aliment. Pharmacol. Ther. 2002, 16 (4) 675-81
49. Blumenthal, R. D.; Leon, E.; Hansen, H. J.; Goldenberg, D. M. Expression patterns of CEACAM5 and CEACAM6 in primary and metastatic cancers BMC Cancer 2007, 7, 2
50. Polanski, M. a. A.;, N. L. A List of Candidate Cancer Biomarkers for Targeted Proteomics Biomarker Insights 2006, 2, 1-48
51. Roncucci, L.; Mora, E.; Mariani, F.; Bursi, S.; Pezzi, A.; Rossi, G.; Pedroni, M.; Luppi, D.; Santoro, L.; Monni, S.; Manenti, A.; Bertani, A.; Merighi, A.; Benatti, P.; Di Gregorio, C.; de Leon, P. M. Myeloperoxidase- positive cell infiltration in colorectal carcinogenesis as indicator of colorectal cancer risk Cancer Epidemiol. Biomarkers Prev. 2008, 17 (9) 2291-7
52. Lee, H. J.; Lee, E. K.; Lee, K. J.; Hong, S. W.; Yoon, Y.; Kim, J. S. Ectopic expression of neutrophil gelatinase-associated lipocalin suppresses the invasion and liver metastasis of colon cancer cells Int. J. Cancer 2006, 118 (10) 2490-7
53. Nielsen, B. S.; Borregaard, N.; Bundgaard, J. R.; Timshel, S.; Sehested, M.; Kjeldsen, L. Induction of NGAL synthesis in epithelial cells of human colorectal neoplasia and inflammatory bowel diseases Gut 1996, 38 (3) 414-20
54. Zhang, X. F.; Zhang, Y.; Zhang, X. H.; Zhou, S. M.; Yang, G. G.; Wang, O. C.; Guo, G. L.; Yang, G. Y.; Hu, X. Q. Clinical significance of Neutrophil gelatinase-associated lipocalin(NGAL) expression in primary rectal cancer BMC Cancer 2009, 9, 134
55. Kronborg, O.; Ugstad, M.; Fuglerud, P.; Johne, B.; Hardcastle, J.; Scholefield, J. H.; Vellacott, K.; Moshakis, V.; Reynolds, J. R. Faecal calprotectin levels in a high risk population for colorectal neoplasia Gut 2000, 46 (6) 795-800
56. Gilbert, J. A.; Ahlquist, D. A.; Mahoney, D. W.; Zinsmeister, A. R.; Rubin, J.; Ellefson, R. D. Fecal marker variability in colorectal cancer: calprotectin versus hemoglobin Scand. J. Gastroenterol. 1996, 31 (10) 1001-5
57. Kim, H.-J.; Kang, H. J.; Lee, H.; Lee, S.-T.; Yu, M.-H.; Kim, H.; Lee, C. Identification of S100A8 and S100A9 as Serological Markers for Colorectal Cancer J. Proteome Res. 2009, 8 (3) 1368-79
58. Stossel, T. P.; Condeelis, J.; Cooley, L.; Hartwig, J. H.; Noegel, A.; Schleicher, M.; Shapiro, S. S. Filamins as integrators of cell mechanics and signalling Nat. Rev. Mol. Cell Biol. 2001, 2 (2) 138-45
59. Stulik, J.; Osterreicher, J.; Koupilova, K.; Knizek, J.; Bures, J.; Jandik, P.; Langr, F.; Dedic, K.; Schafer, B. W.; Heizmann, C. W. Differential expression of the Ca2+ binding S100A6 protein in normal, preneoplastic and neoplastic colon mucosa Eur. J. Cancer 2000, 36 (8) 1050-9
60. Otsuka, M.; Kato, M.; Yoshikawa, T.; Chen, H.; Brown, E. J.; Masuho, Y.; Omata, M.; Seki, N. Differential expression of the L-plastin gene in human colorectal cancer progression and metastasis Biochem. Biophys. Res. Commun. 2001, 289 (4) 876-81
61. Furuta, K.; Ikeda, M.; Nakayama, Y.; Nakamura, K.; Tanaka, M.; Hamasaki, N.; Himeno, M.; Hamilton, S. R.; August, J. T. Expression of lysosome-associated membrane proteins in human colorectal neoplasms and inflammatory diseases Am. J. Pathol. 2001, 159 (2) 449-55