Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer

PLoS ONE

Volumn 3, Issue 11, 2008, Pages

  Yang, Yongliang ^a   Iyer, Lakshmanan K ^b   Adelstein, S James ^a   Kassis, Amin I ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; BRCA1 PROTEIN; BRCA2 PROTEIN; CERULOPLASMIN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; HERMES ANTIGEN; HYALURONIC ACID BINDING PROTEIN; INTERSTITIAL COLLAGENASE; NOTCH4 RECEPTOR; PROSTATE SPECIFIC ANTIGEN; SOMATOMEDIN B; TUMOR MARKER; TUMOR PROTEIN;

ARTICLE; BLOOD SAMPLING; BREAST CANCER; COLON CANCER; COMPUTER PROGRAM; DATA MINING; DIAGNOSTIC ACCURACY; DIFFERENTIAL DIAGNOSIS; EARLY DIAGNOSIS; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENETIC ANALYSIS; HISTOPATHOLOGY; HUMAN; LUNG CANCER; MALIGNANT NEOPLASTIC DISEASE; MARKER GENE; MICROARRAY ANALYSIS; OVARY CANCER; PANCREAS CANCER; PROGNOSIS; PROSTATE CANCER; UPREGULATION; BLOOD; BREAST TUMOR; CARCINOMA; COLON TUMOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; LUNG TUMOR; MALE; NEOPLASM; OVARY TUMOR; PANCREAS TUMOR; PROSTATE TUMOR; TUMOR EMBOLISM;

BREAST NEOPLASMS; CARCINOMA; COLONIC NEOPLASMS; DATABASES, GENETIC; EARLY DIAGNOSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MICROARRAY ANALYSIS; NEOPLASM PROTEINS; NEOPLASMS; NEOPLASTIC CELLS, CIRCULATING; OVARIAN NEOPLASMS; PANCREATIC NEOPLASMS; PROSTATIC NEOPLASMS; TUMOR MARKERS, BIOLOGICAL; UP-REGULATION;

EID: 56349096465     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003661     Document Type: Article

References (60)

1. Zhou W, Sokoll LJ, Bruzek DJ, Zhang L, Velculescu VE, et al. (1998) Identifying markers for pancreatic cancer by gene expression analysis. Cancer Epidemiol Biomarkers Prev 7: 109-112.
2. Liotta LA, Ferrari M, Petricoin E (2003) Clinical proteomics: written in blood. Nature 425: 905.
3. Osman I, Bajorin DF, Sun T-T, Zhong H, Douglas D, et al. (2006) Novel blood biomarkers of human urinary bladder cancer. Clin Cancer Res 12: 3374-3380.
4. Welsh JB, Sapinoso LM, Kern SG, Brown DA, Liu T, et al. (2003) Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc Natl Acad Sci USA 100: 3410-3415.
5. Rhodes DR, Chinnaiyan AM (2004) Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann NY Acad Sci 1020: 32-40.
6. Campagne F, Skrabanek L (2006) Mining expressed sequence tags identifies cancer markers of clinical interest. BMC Bioinformatics 7: 481.
7. Cho WCS (2007) Contribution of oncoproteomics to cancer biomarker discovery. Mol Cancer 6: 25.
8. Kirby J, Heath PR, Shaw PJ, Handy FC (2007) Gene expression assays. AdvClin Chem 44: 247-292.
9. Li S, Becich MJ, Gilbertson J (2004) Microarray data mining using Gene Ontology. Medinfo 107: 778-782.
10. Chen K, Wang K, Kirichian AM, Al Aowad AF, Iyer LK, et al. (2006) In silico design, synthesis, and biological evaluation of radioiodinated quinazolinone derivatives for alkaline phosphatase-mediated cancer diagnosis and therapy. Mol Cancer Ther 5: 3001-3013.
11. Pospisil P, Iyer LK, Adelstein SJ, Kassis AI (2006) A combined approach to data mining of textual and structured data to identify cancer-related targets. BMC Bioinformatics 7: 354.
12. Pospisil P, Wang K, Al Aowad AF, Iyer LK, Adelstein SJ, et al. (2007) computational modeling and experimental evaluation of a novel prodrug for targeting the extracellular space of prostate tumors. Cancer Res 67: 2197-2205.
13. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, et al. (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9: 166-180.
14. Ingenuity® Systems, Ingenuity Pathway Analysis (IPA).
15. Basil CF, Zhao Y, Zavaglia K, Jin P, Panelli MC, et al. (2006) Common cancer biomarkers. Cancer Res 66: 2953-2961.
16. Liu JJ, Cutler G, Li W, Pan Z, Peng S, et al. (2005) Multiclass cancer classification and biomarker discovery using GA-based algorithms. Bioinformatics 21: 2691-2697.
17. Tricoli JV, Schoenfeldt M, Conley BA (2004) Detection of prostate cancer and predicting progression: current and future diagnostic markers. Clin Cancer Res 10: 3943-3953.
18. Troyer DA, Mubiru J, Leach RJ, Naylor SL (2004) Promise and challenge:markers of prostate cancer detection, diagnosis and prognosis. Dis Markers 20: 117-128.
19. Gene Expression Omnibus (GEO) [http://www.ncbi.nlm.nih.gov/geo/].
20. Stanford MicroArray Database (SMD) [http://genome-www5.stanford.edu/].
21. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300.
22. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
23. Holzman T, Kolker E (2004) Statistical analysis of global gene expression data: some practical considerations. Curr Opin Biotechnol 15: 52-57.
24. The Gene Ontology AmiGO [http://amigo.geneontology.org/].
25. iHOP [http://www.ihop-net.org/].
26. Ransohoff DF (2003) Developing molecular biomarkers for cancer. Science 299: 1679-1680.
27. Díamandis EP (2004) How are we going to discover new cancer biomarkers? A proteomic approach for bladder cancer. Clin Chem 50: 793-795.
28. Ross JS, Fletcher JA, Linette GP, Stec J, Clark E, et al. (2003) The HER-2/neu gene and protein in breast cancer 2003: biomarker and target of therapy. Oncologist 8: 307-325.
29. Algü H, Wagner M, Lesina M, Schmid RM (2007) Overexpression of ErbB2 in the exocrine pancreas induces an inflammatory response but not increased proliferation. Int J Cancer 121: 1410-1416.
30. Ross JS, Linette GP, Stec J, Clark E, Ayers M, et al. (2003) Breast cancer biomarkers and molecular medicine. Expert Rev Mol Diagn 3: 573-585.
31. Macleod K, Mullen P, Sewell J, Rabiasz G, Lawrie S, et al. (2005) Altered erbB receptor signaling and gene expression in cisplatin-resistant ovarian cancer. Cancer Res 65: 6789-6800.
32. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266: 66-71.
33. Venkitaraman AR (2002) Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell 108: 171-182.
34. Esteva FJ, Hortobagyi GN (2004) Prognostic molecular markers in early breast cancer. Breast Cancer Res 6: 109-118.
35. Sowter HM, Ashworth A (2005) BRCA1 and BRCA2 as ovarian cancer susceptibility genes. Carcinogenesis 26: 1651-1656.
36. Thompson IM, Pauler DK, Goodman PJ, Tangen CM, Lucia MS, et al. (2004) Prevalence of prostate cancer among men with a prostate-specific antigen level ≤4.0 ng per milliliter. N Engl J Med 350: 2239-2246.
37. Yu H, Giai M, Diamandis EP, Katsaros D, Sutherland DJA, et al. (1995) Prostate-specific antigen is a new favorable prognostic indicator for women with breast cancer. Cancer Res 55: 2104-2110.
38. Sumiya J, Asakawa S, Tobe T, Hashimoto K, Saguchi K, et al. (1997) Isolation and characterization of the plasma hyaluronan-binding protein (PHBP) gene (HABP2). J Biochem 122: 983-990.
39. Wang K, Liu N, Radulovich N, Wigle DA, Johnston MR, et al. (2002) Novel candidate tumor marker genes for lung adenocarcinoma. Oncogene 21: 7598-7604.
40. Csernus VJ, Schally AV, Kiaris H, Armatis P (1999) Inhibition of growth, production of insulin-like growth factor-II (IGF-II), and expression of IGF-II mRNA of human cancer cell lines by antagonistic analogs of growth hormone-releasing hormone in vitro. Proc Natl Acad Sci USA 96: 3098-3103.
41. Zumkeller W (2001) IGFs and IGFBPs: surrogate markers for diagnosis and surveillance of tumour growth? J Clin Pathol Mol Pathol 54: 285-288.
42. Mor G, Visintin I, Lai Y, Zhao H, Schwartz P, et al. (2005) Serum protein markers for early detetion of ovarian cancer. Proc Natl Acad Sci USA 102: 7677-7682.
43. Sciacca L, Costantino A, Pandini G, Mineo R, Frasca F, et al. (1999) Insulin receptor activation by IGF-II in breast cancers: evidence for a new autocrine/ paracrine mechanism. Oncogene 18: 2471-2479.
44. Yu H, Spitz MR, Mistry J, Gu J, Hong WK, et al. (1999) Plasma levels of insulin-like growth factor-I and lung cancer risk: a case-control analysis. J Natl Cancer Inst 91: 151-156.
45. Hoeflich A, Reisinger R, Lahm H, Kiess W, Blum WF, et al. (2001) Insulin-like growth factor -binding protein-2 in tumorigenesis: protector or promoter? Cancer Res 61: 8601-8610.
46. Baker M (2005) In biomarkers we trust? Nat Biotechnol 23: 297-304.
47. Koshiba T, Hosotani R, Wada M, Fujimoto K, Lee J-U, et al. (1997) Detection of matrix metalloproteinase activity in human pancreatic cancer. Surg Today 27: 302-304.
48. Ellenrieder V, Alber B, Lacher U, Hendler SF, Menke A, et al. (2000) Role of MT-MMPs and MMP-2 in pancreatic cancer progression. Int J Cancer 85: 14-20.
49. Bloomston M, Zervos EE, Rosemurgy ASI (2002) Matrix metalloproteinases and their role in pancreatic cancer: a review of preclinical studies and clinical trials. Ann Surg Oncol 9: 668-674.
50. Migita T, Sato E, Saito K, Mizoi T, Shiiba K, et al. (1999) Differing expression of MMPs-1 and -9 and urokinase receptor between diffuse -and intestinal-type gastric carcinoma. Int J Cancer 84: 74-79.
51. Su L, Zhou W, Park S, Wain JC, Lynch TJ, et al. (2005) Matrix metalloproteinase-1 promoter polymorphism and lung cancer risk. Cancer Epidemiol Biomarkers Prev 14: 567-570.
52. Sunami E, Tsuno N, Osada T, Saito S, Kitayama J, et al. (2000) MMP-1 is a prognostic marker for hematogenous metastasis of colorectal cancer. Oncologist 5: 108-114.
53. Masson D, Denis MG, Denis M, Blanchard D, Loirat MJ, et al. (1999) Soluble CD44: quantification and molecular repartition in plasma of patients with colorectal cancer. Br J Cancer 80: 1995-2000.
54. Kim H-R, Wheeler MA, Wilson CM, Iida J, Eng D, et al. (2004) Hyaluronan facilitates invasion of colon carcinoma cells in vitro via interaction with CD44. Cancer Res 64: 4569-4576.
55. Sengupta S, Wehbe C, Majors AK, Ketterer ME, DiBello PM, et al. (2001) Relative roles of albumin and ceruloplasmin in the formation of homocystine, homocystine-cystine-mixed disulfide, and cystine in circulation. J Biol Chem 276: 46896-46904.
56. Hough CD, Cho KR, Zonderman AB, Schwartz DR, Morin PJ (2001) Coordinately up-regulated genes in ovarian cancer. Cancer Res 61: 3869-3876.
57. Miyamoto Y, Maitra A, Ghosh B, Zechner U, Argani P, et al. (2003) Notch mediates TGFa-induced changes in epithelial differentiation during pancreatic tumorigenesis. Cancer Cell 3: 565-576.
58. Garber K (2007) Arrested development? Notch emerges as new cancer drug target. J Natl Cancer Inst 99: 1284-1285.
59. Crnogorac-Jurcevic T, Efthimiou E, Nielsen T, Loader J, Terris B, et al. (2002) Expression profiling of microdissected pancreatic adenocarcinomas. Oncogene 21: 4587-4594.
60. He YD (2006) Genomic approach to biomarker identification and its recent applications. Cancer Biomark 2: 103-133.