Strategies for discovering novel cancer biomarkers through utilization of emerging technologies

Nature Clinical Practice Oncology

Volumn 5, Issue 10, 2008, Pages 588-599

  Kulasingam, Vathany ^a   Diamandis, Eleftherios P ^a  

^a MOUNT SINAI HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA FETOPROTEIN; CA 125 ANTIGEN; CA 19-9 ANTIGEN; CALCITONIN; CARCINOEMBRYONIC ANTIGEN; CHORIONIC GONADOTROPIN BETA SUBUNIT; COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; EPIDIDYMAL SECRETORY PROTEIN; EPIDIDYMAL SECRETORY PROTEIN 4; ESTROGEN RECEPTOR; LACTATE DEHYDROGENASE; PROGESTERONE RECEPTOR; PROSTATE SPECIFIC ANTIGEN; PROTEOME; THYROGLOBULIN; TRASTUZUMAB; TUMOR MARKER; UNCLASSIFIED DRUG;

ANGIOGENESIS; BODY FLUID; CANCER CLASSIFICATION; CANCER INVASION; CANCER SCREENING; CANCER STAGING; CANCER THERAPY; DIAGNOSTIC VALUE; DISEASE MARKER; DNA MICROARRAY; DRUG RESPONSE; DRUG TARGETING; EARLY DIAGNOSIS; GENE EXPRESSION PROFILING; GENE OVEREXPRESSION; HUMAN; MALIGNANT NEOPLASTIC DISEASE; MASS SPECTROMETRY; MOLECULAR DYNAMICS; OVARY CANCER; PEPTIDOMICS; PRIORITY JOURNAL; PROGNOSIS; PROSTATE CANCER; PROTEIN MICROARRAY; PROTEIN SECRETION; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SENSITIVITY AND SPECIFICITY; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TISSUE INJURY; TREATMENT RESPONSE;

GENE EXPRESSION PROFILING; HUMANS; MASS SPECTROMETRY; NEOPLASM PROTEINS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOMICS; SENSITIVITY AND SPECIFICITY; TECHNOLOGY; TUMOR MARKERS, BIOLOGICAL;

EID: 53849144620     PISSN: 17434254     EISSN: 17434262     Source Type: Journal    
DOI: 10.1038/ncponc1187     Document Type: Review

References (93)

1. Jemal A et al. (2007) Cancer statistics, 2007. CA Cancer J Clin 57: 43-66
2. Etzioni R et al. (2003) The case for early detection. Nat Rev Cancer 3: 243-252
3. Hayes DF et al. (1996) Tumor marker utility grading system: A framework to evaluate clinical utility of tumor markers. J Natl Cancer Inst 88: 1456-1466
4. Jones HB (1848) On a new substance occuring in the urine with mollities ossium. Phil Trans R Soc Lond 138: 55-62
5. Abelev GI et al. (1963) Production of embryonal alpha-globulin by transplantable mouse hepatomas. Transplantation 1: 174-180
6. Gold P and Freedman SO (1965) Specific carcinoembryonic antigens of the human digestive system. J Exp Med 122: 467-481
7. Bast RC Jr et al. (1981) Reactivity of a monoclonal antibody with human ovarian carcinoma. J Clin Invest 68: 1331-1337
8. Papsidero LD et al. (1980) A prostate antigen in sera of prostatic cancer patients. Cancer Res 40: 2428-2432
9. Anderson NL and Anderson NG (2002) The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1: 845-867
10. Tomlins SA et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644-648
11. Ono K et al. (2000) Identification by cDNA microarray of genes involved in ovarian carcinogenesis. Cancer Res 60: 5007-5011
12. Welsh JB et al. (2001) Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci USA 98: 1176-1181
13. Hellstrom I et al. (2003) The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. Cancer Res 63: 3695-3700
14. Galgano MT et al. (2006) Comprehensive analysis of HE4 expression in normal and malignant human tissues. Mod Pathol 19: 847-853
15. Jarjanazi H et al. (2008) Biological implications of SNPs in signal peptide domains of human proteins. Proteins 70: 394-403
16. Abelev GI and Eraiser TL (1999) Cellular aspects of alpha-fetoprotein reexpression in tumors. Semin Cancer Biol 9: 95-107
17. Slamon DJ et al. (1987) Human breast cancer: Correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235: 177-182
18. Shak S (1999) Overview of the trastuzumab (Herceptin) anti-HER2 monoclonal antibody clinical program in HER2-overexpressing metastatic breast cancer. Herceptin Multinational Investigator Study Group. Semin Oncol 26: 71-77
19. Molina R et al. (1996) C-erbB-2 oncoprotein in the sera and tissue of patients with breast cancer: Utility in prognosis. Anticancer Res 16: 2295-2300
20. Stacker SA et al. (2002) Lymphangiogenesis and cancer metastasis. Nat Rev Cancer 2: 573-583
21. Quackenbush J (2006) Microarray analysis and tumor classification. N Engl J Med 354: 2463-2472
22. Eisen MB et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868
23. Golub TR et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286: 531-537
24. Perou CM et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747-752
25. Alizadeh AA et al. (2001) Towards a novel classification of human malignancies based on gene expression patterns. J Pathol 195 41-52
26. Weigelt B et al. (2005) Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res 65: 9155-9158
27. Alizadeh AA et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403 503-511
28. Rosenwald A et al. (2002) The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 346: 1937-1947
29. Pomeroy SL et al. (2002) Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415 436-442
30. lizuka N et al. (2004) Predicting individual outcomes in hepatocellular carcinoma. Lancet 364: 1837-1839
31. Chen HY et al. (2007) A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med 356: 11-20
32. van de Vijver MJ et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009
33. Paik S et al. (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351: 2817-2826
34. Pollack JR (2007) A perspective on DNA microarrays in pathology research and practice. Am J Pathol 171: 375-385
35. Michiels S et al. (2005) Prediction of cancer outcome with microarrays: A multiple random validation strategy. Lancet 365 488-492
36. Ioannidis JP (2005) Microarrays and molecular research: Noise discovery? Lancet 365: 454-455
37. Diamandis EP et al. (2006) National Academy of Clinical Biochemistry Guidelines: The Use of Microarrays in Cancer Diagnostics. American Association for Clinical Chemistry. 2006. Ref Type: Electronic Citation [www.aacc.org/NR/rdonlyres/E4CF9D42-B055-4377-A02E-F0BD3856C456/ 0/chp4a_microarray.pdf]
38. Domon B and Aebersold R (2006) Mass spectrometry and protein analysis. Science 312: 212-217
39. Wulfkuhle JD et al. (2003) Proteomic approaches to the diagnosis, treatment, and monitoring of cancer. Adv Exp Med Biol 532: 59-68
40. Petricoin EF et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359: 572-577
41. Li J et al. (2002) Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48: 1296-1304
42. Petricoin EF III et al. (2002) Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 94: 1576-1578
43. Chen YD et al. (2004) Artificial neural networks analysis of surface-enhanced laser desorption/ionization mass spectra of serum protein pattern distinguishes colorectal cancer from healthy population. Clin Cancer Res 10: 8380-8385
44. Paradis V et al. (2005) Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology 41: 40-47
45. Tolson J et al. (2004) Serum protein profiling by SELDI mass spectrometry: Detection of multiple variants of serum amyloid alpha in renal cancer patients. Lab Invest 84: 845-856
46. Rosty C et al. (2002) Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res 62: 1868-1875
47. Wadsworth JT et al. (2004) Identification of patients with head and neck cancer using serum protein profiles. Arch Otolaryngol Head Neck Surg 130: 98-104
48. Diamandis EP (2003) Point: ProteomiD patterns in biological fluids: do they represent the future of cancer diagnostics? Clin Chem 49 1272-1275
49. Karsan A et al. (2005) Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin Chem 51: 1525-1528
50. Banks RE et al. (2005) Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin Chem 51: 1637-1649
51. Ransohoff DF (2005) Lessons from controversy: Ovarian cancer screening and serum proteomics. J Natl Cancer Inst 97: 315-319
52. Baggerly KA et al. (2005) Signal in noise: Evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst 97: 307-309
53. Chan DW et al. (2006) National Academy of Clinical Biochemistry Guidelines: The Use of MALDI-TOF Mass Spectrometry Profiling to Diagnose Cancer. American Association for Clinical Chemistry. 2006. Ref Type: Electronic Citation [www.aacc.org/NR/rdonlyres/ 45357D4E-FA88-4997-B8A6-74BFE31A3D49/0/chp4b_mass_spec.pdf]
54. Lopez MF et al. (2005) High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures. Clin Chem 51: 1946-1954
55. Liotta LA et al. (2003) Clinical proteomics: Written in blood. Nature 425: 905
56. Tirumalai RS et al. (2003) Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2: 1096-1103
57. Harper RG et al. (2004) Low-molecular-weight human serum proteome using ultrafiltration, isoelectric focusing, and mass spectrometry. Electrophoresis 25: 1299-1306
58. Rai DK et al. (2004) Accurate mass measurement and tandem mass spectrometry of intact globin chains identify the low proportion variant hemoglobin Lepore-Boston-Washington from the blood of a heterozygote. J Mass Spectrom 39: 289-294
59. Villanueva J etal. (2006) Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 116: 271-284
60. Lopez MF et al. (2007) A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples. Clin Chem 53 1067-1074
61. Koomen JM et al. (2005) Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res 4: 972-981
62. Diamandis EP (2006) Peptidomics for cancer diagnosis: Present and future. J Proteome Res 5: 2079-2082
63. Borgono CA and Diamandis EP (2004) The emerging roles of human tissue kallikreins in cancer. Nat Rev Cancer 4: 876-890
64. Rittenhouse HG et al. (1998) Human Kallikrein 2 (hK2) and prostate-specific antigen (PSA): Two closely related, but distinct, kallikreins in the prostate. Crit Rev Clin Lab Sci 35: 275-368
65. Diamandis EP et al. (2003) Human kallikrein 6 (hK6): A new potential serum biomarker for diagnosis and prognosis of ovarian carcinoma. J Clin Oncol 21: 1035-1043
66. Liotta LA and Kohn EC (2001) The microenvironment of the tumour-host interface. Nature 411: 375-379
67. Jung YD et al. (2002) The role of the microenvironment and intercellular cross-talk in tumor angiogenesis. Semin Cancer Biol 12: 105-112
68. Celis JE et al. (2004) Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: A novel resource for biomarker and therapeutic target discovery. Mol Cell Proteomics 3: 327-344
69. Wang X et al. (2005) Autoantibody signatures in prostate cancer. N Engl J Med 353: 1224-1235
70. Nowell PC and Hungerford DA (1960) Chromosome studies on normal and leukemic human leukocytes. J Natl Cancer Inst 25: 85-109
71. Caprioli RM (2005) Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy. Cancer Res 65: 10642-10645
72. Yanagisawa K et al. (2003) Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362: 433-439
73. Faca V et al. (2007) Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 6: 3558-3565
74. Kuick R et al. (2007) Discovery of cancer biomarkers through the use of mouse models. Cancer Lett 249: 40-48
75. Whiteaker JR et al. (2007) Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 6: 3962-3975
76. Pepe MS et al. (2001) Phases of biomarker development for early detection of cancer. J Natl Cancer Inst 93: 1054-1061
77. Bast RC Jr et al. (2001) 2000 update of recommendations for the use of tumor markers in breast and colorectal cancer: Clinical practice guidelines of the American Society of Clinical Oncology. J Clin Oncol 19: 1865-1878
78. Finne P et al. (2000) Predicting the outcome of prostate biopsy in screen-positive men by a multilayer perceptron network. Urology 56: 418-422
79. Stephan C et al. (2002) Multicenter evaluation of an artificial neural network to increase the prostate cancer detection rate and reduce unnecessary biopsies. Clin Chem 48: 1279-1287
80. Diamandis EP et al. (2002) Tumor Markers: Physiology, Pathobiology, Technology, and Clinical Applications. Washington, DC: AACC Press
81. Melvin KE et al. (1971) Early diagnosis of medullary carcinoma of the thyroid gland by means of calcitonin assay. N Engl J Med 285: 1115-1120
82. Sturgeon C (2002) Practice guidelines for tumor marker use in the clinic. Clin Chem 48: 1151-1159
83. Kufe D et al. (1984) Differential reactivity of a novel monoclonal antibody (DF3) with human malignant versus benign breast tumors. Hybridoma 3: 223-232
84. Hilkens J et al. (1984) Monoclonal antibodies against human milk-fat globule membranes detecting differentiation antigens of the mammary gland and its tumors. Int J Cancer 34: 197-206
85. Koprowski H et al. (1979) Colorectal carcinoma antigens detected by hybridoma antibodies. Somatic Cell Genet 5: 957-971
86. Ludwig JA and Weinstein JN (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 5: 845-856
87. McGuire WL et al. (1977) Current status of estrogen and progesterone receptors in breast cancer. Cancer 39: 2934-2947
88. Coussens L et al. (1985) Tyrosine kinase receptor with extensive homology to EGF receptor shares chromosomal location with neu oncogene. Science 230: 1132-1139
89. Yamamoto T et al. (1986) Similarity of protein encoded by the human c-erb-B-2 gene to epidermal growth factor receptor. Nature 319: 230-234
90. Bagshawe KD et al. (1980) Markers in gynaecological cancer. Arch Gynecol 229: 303-310
91. Hill BR and Levi C (1954) Elevation of a serum component in neoplastic disease. Cancer Res 14: 513-515
92. Wang MC et al. (1979) Purification of a human prostate specific antigen. Invest Urol 17: 159-163
93. Carayanniotis G and Rao VP (1977) Searching for pathogenic epitopes in thyroglobulin: Parameters and caveats. Immunol Today 18: 83-88