Current status and prospects of clinical proteomics studies on detection of colorectal cancer: Hopes and fears

World Journal of Gastroenterology

Volumn 12, Issue 41, 2006, Pages 6594-6601

  de Noo, M E ^a   Tollenaar, R A E M ^a   Deelder, A M ^a   Bouwman, L H ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Biomarkers; Colorectal cancer; Diagnosis; Protein profilling; Proteomics; Statistical issues

Indexed keywords

BIOLOGICAL MARKER; CARCINOEMBRYONIC ANTIGEN; ONCOPROTEIN; PROTEOME;

BODY FLUID; CANCER CLASSIFICATION; CANCER MORTALITY; CANCER RESEARCH; CAUSE OF DEATH; COLORECTAL CANCER; COLORECTAL CARCINOMA; DIAGNOSTIC PROCEDURE; DIAGNOSTIC VALUE; DISEASE ACTIVITY; DISEASE COURSE; EARLY DIAGNOSIS; EDITORIAL; HUMAN; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; ONCOLOGY; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN MODIFICATION; PROTEIN SECRETION; PROTEIN SYNTHESIS; PROTEOMICS; RELIABILITY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 33751288840     PISSN: 10079327     EISSN: None     Source Type: Journal    
DOI: 10.3748/wjg.v12.i41.6594     Document Type: Editorial

References (69)

1. Chambers G, Lawrie L, Cash P, Murray GI. Proteomics: a new approach to the study of disease. J Pathol 2000; 192: 280-288
2. 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
3. Weitz J, Koch M, Debus J, Hohler T, Galle PR, Buchler MW. Colorectal cancer. Lancet 2005; 365: 153-165
4. Russo MW, Wei JT, Thiny MT, Gangarosa LM, Brown A, Ringel Y, Shaheen NJ, Sandler RS. Digestive and liver diseases statistics, 2004. Gastroenterology 2004; 126: 1448-1453
5. Jemal A, Tiwari RC, Murray T, Ghafoor A, Samuels A, Ward E, Feuer EJ, Thun MJ. Cancer statistics, 2004. CA Cancer J Clin 2004; 54: 8-29
6. Pfister DG, Benson AB 3rd, Somerfield MR. Clinical practice. Surveillance strategies after curative treatment of colorectal cancer. N Engl J Med 2004; 350: 2375-2382
7. Liefers GJ, Tollenaar RA. Cancer genetics and their application to individualised medicine. Eur J Cancer 2002; 38: 872-879
8. Ruo L, Gougoutas C, Paty PB, Guillem JG, Cohen AM, Wong WD. Elective bowel resection for incurable stage IV colorectal cancer: prognostic variables for asymptomatic patients. J Am Coll Surg 2003; 196: 722-728
9. Gill S, Sinicrope FA. Colorectal cancer prevention: is an ounce of prevention worth a pound of cure? Semin Oncol 2005; 32: 24-34
10. Hawk ET, Levin B. Colorectal cancer prevention. J Clin Oncol 2005; 23: 378-391
11. Gion M, Daidone MG. Circulating biomarkers from tumour bulk to tumour machinery: promises and pitfalls. Eur J Cancer 2004; 40: 2613-2622
12. Duffy MJ, van Dalen A, Haglund C, Hansson L, Klapdor R, Lamerz R, Nilsson O, Sturgeon C, Topolcan O. Clinical utility of biochemical markers in colorectal cancer: European Group on Tumour Markers (EGTM) guidelines. Eur J Cancer 2003; 39: 718-727
13. Fletcher RH. Rationale for combining different screening strategies. Gastrointest Endosc Clin N Am 2002; 12: 53-63
14. Winawer S, Fletcher R, Rex D, Bond J, Burt R, Ferrucci J, Ganiats T, Levin T, Woolf S, Johnson D, Kirk L, Litin S, Simmang C. Colorectal cancer screening and surveillance: clinical guidelines and rationale-Update based on new evidence. Gastroenterology 2003; 124: 544-560
15. Ouyang DL, Chen JJ, Getzenberg RH, Schoen RE. Noninvasive testing for colorectal cancer: a review. Am J Gastroenterol 2005; 100: 1393-1403
16. Pignone M, Rich M, Teutsch SM, Berg AO, Lohr KN. Screening for colorectal cancer in adults at average risk: a summary of the evidence for the U.S. Preventive Services Task Force. Ann Intern Med 2002; 137:132-141
17. Ransohoff DF, Lang CA. Screening for colorectal cancer with the fecal occult blood test: a background paper. American College of Physicians. Ann Intern Med 1997; 126: 811-822
18. Ransohoff DF. Colon cancer screening in 2005: status and challenges. Gastroenterology 2005; 128: 1685-1695
19. Adam BL, Qu Y, Davis JW, Ward MD, Clements MA, Cazares LH, Semmes OJ, Schellhammer PF, Yasui Y, Feng Z, Wright GL Jr. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 2002; 62: 3609-3614
20. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, Liotta LA. Use of proteornic patterns in serum to identify ovarian cancer. Lancet 2002; 359: 572-577
21. Rai AJ, Zhang Z, Rosenzweig J, Shih IeM, Pham T, Fung ET, Sokoll LJ, Chan DW. Proteomic approaches to tumor marker discovery. Arch Pathol Lab Med 2002; 126: 1518-1526
22. Yanagisawa K, Shyr Y, Xu BJ, Massion PP, Larsen PH, White BC, Roberts JR, Edgerton M, Gonzalez A, Nadaf S, Moore JH, Caprioli RM, Carbone DP. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003; 362: 433-439
23. Petricoin EF, Liotta LA. Proteomic analysis at the bedside: early detection of cancer. Trends Biotechnol 2002; 20: S30-S34
24. Wulfkuhle JD, Liotta LA, Petricoin EF. Proteomic applications for the early detection of cancer. Nat Rev Cancer 2003; 3: 267-275
25. Petricoin EE, Paweletz CP, Liotta LA. Clinical applications of proteomics: proteomic pattern diagnostics. J Mammary Gland Biol Neoplasia 2002; 7: 433-440
26. Boguski MS, McIntosh MW. Biomedical informatics for proteomics. Nature 2003; 422: 233-237
27. Diamandis EP. Re: Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2003; 95: 489-490; author reply 490-491
28. Diamandis EP. Proteomic patterns in serum and identification of ovarian cancer. Lancet 2002; 360: 170; author reply 170-171
29. Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 2003; 4: 24
30. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 2004; 20: 777-785
31. de Noo ME, Tollenaar RAEM, Ozalp A, Kuppen PJK, Bladergroen MR, and Deelder AM. Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry. Anal Chem 2005; 77: 7232-7241
32. Villanueva J, Philip J, Entenberg D, Chaparro CA, Tanwar MK, Holland EC, Tempst P. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal Chem 2004; 76: 1560-1570
33. Baumann S, Ceglarek U, Fiedler GM, Lembcke J, Leichtle A, Thiery J. Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chem 2005; 51: 973-980
34. West-Nielsen M, Hogdall EV, Marchiori E, Hogdall CK, Schou C, Heegaard NH. Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem 2005; 77: 5114-5123
35. Baggerly KA, Morris JS, Wang J, Gold D, Xiao LC, Coombes KR. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples, Proteomics 2003; 3:1667-1672
36. Yasui Y, Pepe K, Thompson ML, Adam BL, Wright GL Jr, Qu Y, Potter JD, Winget M, Thornquist M, Feng Z. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics 2003; 4: 449-463
37. Eilers PH. A perfect smoother. Anal Chem 2003; 75: 3631-3636
38. Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling - a young technology begins to mature. Nat Biotechnol 2005; 23:291-292
39. Ransohoff DF. Rules of evidence for cancer molecular-marker discovery and validation. Nat Rev Cancer 2004; 4: 309-314
40. Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 2004; 96: 353-356
41. de Noo ME, Mertens BJ, Ozalp A, Bladergroen MR, van der Werff MP, van de Velde CJ, Deelder AM, Tollenaar RA. Detection of colorectal cancer using MALDI-TOF serum protein profiling. Eur J Cancer 2006; 42: 1068-1076
42. 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
43. Wang X, Zhu W, Pradhan K, Ji C, Ma Y, Semmes OJ, Glimm J, Mitchell J. Feature extraction in the analysis of proteomic mass spectra. Proteomics 2006; 6: 2095-2100
44. Levner I. Feature selection and nearest centroid classification for protein mass spectrometry. BMC Bioinformatics 2005; 6: 68
45. Somorjai RL, Dolenko B, Baumgartner R. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 2003; 19: 1484-1491
46. Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/ mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom 2005; 19: 1624-1636
47. Ye B, Cramer DW, Skates SJ, Gygi SP, Pratomo V, Fu L, Horick NK, Licklider LJ, Schorge JO, Berkowitz RS, Mok SC. Haptoglobin-alpha. subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin Cancer Res 2003; 9: 2904-2911
48. Koomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res 2005; 11: 1110-1118
49. Wang X, Wang E, Kavanagh JJ, Freedman RS. Ovarian cancer, the coagulation pathway, and inflammation. J Transl Med 2005; 3:25
50. Li J, Orlandi R, White CN, Rosenzweig J, Zhao J, Seregni E, Morelli D, Yu Y, Meng XY, Zhang Z, Davidson NE, Fung ET, Chan DW. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin Chem 2005; 51: 9929-2215
51. Diamandis EP, van der Merwe DE. Plasma protein profiling by mass spectrometry for cancer diagnosis: opportunities and limitations. Clin Cancer Res 2005; 11: 963-965
52. Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res 2005; 4: 972-981
53. Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006; 116: 271-284
54. Liotta LA, Petricoin EF. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J Clin Invest 2006; 116: 26-30
55. Matrisian LM, Sledge GW Jr, Mohla S. Extracellular proteolysis and cancer: meeting summary and future directions. Cancer Res 2003; 63: 6105-6109
56. Bank U, Kruger S, Langner J, Roessner A. Review: peptidases and peptidase inhibitors in the pathogenesis of diseases. Disturbances in the ubiquitin-mediated proteolytic system. Protease-antiprotease imbalance in inflammatory reactions. Role of cathepsins in tumour progression. Adv Exp Med Biol 2000; 477: 349-378
57. Song J, Patel M, Rosenzweig CN, Chan-Li Y, Sokoll LJ, Fung ET, Choi-Miura NH, Goggins M, Chan DW, Zhang Z. 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
58. Marshall J, Kupchak P, Zhu W, Yantha J, Vrees T, Furesz S, Jacks K, Smith C, Kireeva I, Zhang R, Takahashi M, Stanton E, Jackowski G. Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J Proteome Res 2003; 2: 361-372
59. Steinert R, Buschmann T, van der Linden M, Fels LM, Lippert H, Reymond MA. The role of proteomics in the diagnosis and outcome prediction in colorectal cancer. Technol Cancer Res Treat 2002; 1: 297-304
60. Yu JK, Chen YD, Zheng S. An integrated approach to the detection of colorectal cancer utilizing proteornics and bioinformatics. World J Gastroenterol 2004; 10: 3127-3131
61. Engwegen JY, Helgason HH, Cats A, Harris N, Bonfrer JM, Schellens JH, Beijnen JH. 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
62. Steinert R, Buschmann T, van der Linden M, Fels LM, Lippert H, Reymond MA. The role of proteomics in the diagnosis and outcome prediction in colorectal cancer. Technol Cancer Res Treat 2002; 1: 297-304
63. Gulmann C, Sheehan KM, Kay EW, Liotta LA, Petricoin EF 3rd. Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. J Pathol 2006; 208: 595-606
64. Miller JC, Zhou H, Kwekel J, Cavallo F, Burke J, Butler EB, Teh BS, Haab BB. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 2003; 3: 56-63
65. 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; 3:243-252
66. Kolch W, Mischak H, Pitt AR. The molecular make-up of a tumour: proteomics in cancer research. Clin Sci (Lond) 2005; 108: 369-383
67. Srinivas PR, Verma M, Zhao Y, Srivastava S. Proteomics for cancer biomarker discovery. Clin Chem 2002; 48: 1160-1169
68. de Noo ME, Liefers GJ, Tollenaar RA. Translational research in prognostic profiling in colorectal cancer. Dig Surg 2005; 22: 276-281
69. Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 2005; 5: 845-856