Biomarkers in the age of omics: Time for a systems biology approach

OMICS A Journal of Integrative Biology

Volumn 15, Issue 3, 2011, Pages 105-112

  Abu Asab, Mones S ^a   Chaouchi, Mohamed ^b   Alesci, Salvatore ^c   Galli, Susana ^a   Laassri, Majid ^d   Cheema, Amrita K ^e   Atouf, Fouad ^f   Vanmeter, John ^b   Amri, Hakima ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b GEORGETOWN UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c PFIZER INC   (United States)

^d CENTER FOR BIOLOGICS EVALUATION AND RESEARCH   (United States)

^e GEORGETOWN UNIVERSITY   (United States)

^f UNITED STATES PHARMACOPEIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

CARCINOGENESIS; CELL HETEROGENEITY; GENE MUTATION; HUMAN; IMMUNOHISTOCHEMISTRY; IMMUNOPATHOLOGY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REVIEW;

BIOLOGICAL MARKERS; GENOMICS; HUMANS; IMMUNOHISTOCHEMISTRY; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 79952526456     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2010.0023     Document Type: Review

References (56)

1. Abelev, G. I., and Eraiser, T. L. (2008). On the path to understanding the nature of cancer. Biochemistry (Moscow) 73, 487-497. (Pubitemid 351775072)
2. Abu-Asab, M. (2009). Microarrays need phylogenetics. Sci STKE (E-Letter, 30 January 2009). Available at: http://stkesciencemagorg/cgi/eletters/ sigtrans;1/51/eg11.
3. Abu-Asab, M., Chaouchi, M., and Amri, H. (2006). Phyloproteomics: what phylogenetic analysis reveals about serum proteomics. J Proteome Res 5, 2236-2240. (Pubitemid 44330816)
4. Abu-Asab, M., Chaouchi, M., and Amri, H. (2008a). Evolutionary medicine: a meaningful connection between omics, disease, and treatment. Proteomics Clin Appl 2, 122-134. (Pubitemid 351284894)
5. Abu-Asab, M. S., Chaouchi, M., and Amri, H. (2008b). Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens. Omics 12, 183-199.
6. Barry, M. J. (2009). Screening for prostate cancer-the controversy that refuses to die. N Engl J Med 360, 1351-1354.
7. Bielas, J. H., Loeb, K. R., Rubin, B. P., True, L. D., and Loeb, L. A. (2006). Human cancers express a mutator phenotype. Proc Natl Acad Sci USA 103, 18238-18242. (Pubitemid 44871642)
8. Briasoulis, E., and Pavlidis, N. (1997). Cancer of unknown primary origin. Oncologist 2, 142-152. (Pubitemid 27263946)
9. Brock, A., Chang, H., and Huang, S. (2009). Non-genetic heterogeneity-a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet 10:336-342.
10. Camin, J., and Sokal, R. (1965). A method for deducing branching sequences in phylogeny. Evolution 19, 311-326.
11. Campbell, P. J., Pleasance, E. D., Stephens, P. J., Dicks, E., Rance, R., et al. (2008). Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci USA 105, 13081-13086.
12. Concato, J., Jain, D., Uchio, E., Risch, H., Li, W. W., and Wells, C. K. (2009). Molecular markers and death from prostate cancer. Ann Intern Med 150, 595-603.
13. Dalerba, P., Cho, R. W., and Clarke, M. F. (2007). Cancer stem cells: models and concepts. Annu Rev Med 58, 267-284. (Pubitemid 46706514)
14. Deo, R. C., and Roth, F. P. (2009). Pathways of the heart. Circ Cardiovasc Genet 2, 303-305.
15. Dowsett, M., and Dunbier, A. K. (2008). Emerging biomarkers and new understanding of traditional markers in personalized therapy for breast cancer. Clin Cancer Res 14, 8019-8026.
16. Felsenstein, J. (1989). PHYLIP: phylogeny inference package (Version 3.2). Cladistics 5, 164-166.
17. Fisher, B., Redmond, C. K., and Fisher, E. R. (2008). Evolution of knowledge related to breast cancer heterogeneity: a 25-year retrospective. J Clin Oncol 26, 2068-2071.
18. Heim-Hall, J., and Yohe, S. L. (2008). Application of immunohistochemistry to soft tissue neoplasms. Arch Pathol Lab Med 132, 476-489. (Pubitemid 351328817)
19. Heng, H. H., Stevens, J. B., Bremer, S. W., Ye, K. J., Liu, G., and Ye, C. J. (2010). The evolutionary mechanism of cancer. J Cell Biochem 6, 1072-1084.
20. Hippo, Y., Taniguchi, H., Tsutsumi, S., Machida, N., Chong, J. M., Fukayama, M., et al. (2002). Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res 62, 233-240. (Pubitemid 34074010)
21. Hoeijmakers, J. H. (2001). Genome maintenance mechanisms for preventing cancer. Nature 411, 366-374. (Pubitemid 32467046)
22. Kaput, J., and Rodriguez, R. L. (2004). Nutritional genomics: the next frontier in the postgenomic era. Physiol Genomics 16, 166-177. (Pubitemid 38420031)
23. Kaiser, J. (2009). Researcher, two universities sued over validity of prostate cancer test. Science 5947, 1484.
24. Kashani-Sabet, M., Rangel, J., Torabian, S., Nosrati, M., Simko, J., Jablons, D. M., et al. (2009). A multi-marker assay to distinguish malignant melanomas from benign nevi. Proc Natl Acad Sci USA 15, 6268-6272.
25. Klein, C. A., and Stoecklein, N. H. (2009). Lessons from an aggressive cancer: evolutionary dynamics in esophageal carcinoma. Cancer Res 69:5285-5288.
26. Knox, S. S. (2010). From "omics" to complex disease: a systems biology approach to gene-environment interactions in cancer. Cancer Cell Int 10, 11.
27. Kolaczkowski, B., and Thornton, J. W. (2004). Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431, 980-984. (Pubitemid 39434418)
28. Lerma, E., Peiro, G., Ramón, T., Fernandez, S., Martinez, D., Pons, C., et al. (2007). Immunohistochemical heterogeneity of breast carcinomas negative for estrogen receptors, progesterone receptors and Her2/neu (basal-like breast carcinomas). Mod Pathol 11, 1200-1207. (Pubitemid 47609069)
29. Loeb, L. A., Bielas, J. H., and Beckman, R. A. (2008). Cancers exhibit a mutator phenotype: clinical implications. Cancer Res 68, 3551-3557; discussion 3557.
30. Loi, S., Haibe-Kains, B., Desmedt, C., Lallemand, F., Tutt, A. M., Gillet, C., et al. (2007). Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 25, 1239-1246. (Pubitemid 46640570)
31. Lyons-Weiler, J., Patel, S., Becich, M. J., and Godfrey, T. E. (2004). Tests for finding complex patterns of differential expression in cancers: towards individualized medicine. BMC Bioinformatics 5, 110.
32. Maher, B. (2008). Personal genomes: the case of the missing heritability. Nature 456, 18-21.
33. Mareel, M., and Leroy, A. (2003). Clinical, cellular, and molecular aspects of cancer invasion. Physiol Rev 83, 337-376. (Pubitemid 36382891)
34. May, M. (2010). Biomarkers still off the mark for detecting breast cancer. Nat Med 16, 3.
35. Morrison, R. S., and Veenstra, T. D. (2008). Biomarker discovery: Has it been worth it so far? Proteomics Clin Appl 2, 1375-1376.
36. Nature. (2008). The big ome. Nature 452, 913-914.
37. Nature. (2010). Valid concerns. Nature 463, 401-402.
38. Oved, K., Eden, E., Akerman, M., Noy, R., Wolchinsky, R., Izhaki, O., et al. (2009). Predicting and controlling the reactivity of immune cell populations against cancer. Mol Syst Biol 5, 265.
39. Partridge, E., Kreimer, A. R., Greenlee, R. T., Williams, C., Xu, J. L., Church, T. R., et al. (2009). Results from four rounds of ovarian cancer screening in a randomized trial. Obstet Gynecol 113, 775-782.
40. Podsypanina, K., Du, Y. C., Jechlinger, M., Beverly, L. J., Hambardzumyan, D., and Varmus, H. (2008). Seeding and propagation of untransformed mouse mammary cells in the lung. Science 321, 1841-1844.
41. Ransohoff, D. F. (2009). Promises and limitations of biomarkers. Rec Results Cancer Res 181, 55-59.
42. Rifai, N., Gillette, M. A., and Carr, S. A. (2006). Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 24, 971-983. (Pubitemid 44215392)
43. Rosai, J., and Ackerman, L. V. (2004). Rosai and Ackerman's surgical pathology. (Mosby, Edinburgh; New York).
44. Roukos, D. H. (2009). Mea Culpa with cancer-targeted therapy: new thinking and new agents design for novel, causal networks-based, personalized biomedicine. Expert Rev Mol Diag 9, 217-221.
45. Sawyers, C. L. (2008). The cancer biomarker problem. Nature 452, 548-552. (Pubitemid 351483368)
46. Schadt, E. E., Friend, S. H., and Shaywitz, D. A. (2009). A network view of disease and compound screening. Nat Rev Drug Discov 8, 286-295.
47. Schaub, N. P., Jones, K. J., Nyalwidhe, J. O., Cazares, L. H., Karbassi, I. D., Semmes, O. J., et al. (2009). Serum proteomic biomarker discovery reflective of stage and obesity in breast cancer patients. J Am Coll Surg 208, 970-978; discussion 978-980.
48. Stefankovic, D., and Vigoda, E. (2007a). Phylogeny of mixture models: robustness of maximum likelihood and non-identifiable distributions. J Comput Biol 14, 156-189. (Pubitemid 46709353)
49. Stefankovic, D., and Vigoda, E. (2007b). Pitfalls of heterogeneous processes for phylogenetic reconstruction. Syst Biol 56, 113-124.
50. Sumer, B., and Gao, J. (2008). Theranostic nanomedicine for cancer. In Nanomedicine (London, England), Vol. 3, pp. 137-140. (Pubitemid 351611851)
51. Takikita, M., Chung, J. Y., and Hewitt, S. M. (2007). Tissue microarrays enabling high-throughput molecular pathology. Curr Opin Biotechnol 18, 318-325. (Pubitemid 47393621)
52. Varambally, S., Yu, J., Laxman, B., Rhodes, D. R., Mehra, R., Tomlins, S. A., et al. (2005). Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell. 8:393-406. (Pubitemid 41579834)
53. Yaffe, M. B. (2008). How to "cell" a genomic or proteomic screen. Sci Signal 1, eg9.
54. Wang, Y., Klijn, J. G., Zhang, Y., Sieuwerts, A. M., Look, M. P., Yang, F., et al. (2005). Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365, 671-679. (Pubitemid 40260888)
55. Warren, J. L., Mariotto, A. B., Meekins, A., Topor, M., and Brown, M. L. (2008). Current and future utilization of services from medical oncologists. J Clin Oncol 26, 3242-3247.
56. Winter, E. E., Goodstadt, L., and Ponting, C. P. (2004). Elevated rates of protein secretion, evolution, and disease among tissuespecific genes. Genome Res 14, 54-61. (Pubitemid 38088525)