Oncogenomics and the development of new cancer therapies

Nature

Volumn 429, Issue 6990, 2004, Pages 469-474

  Strausberg, Robert L ^a   Simpson, Andrew J G ^b   Old, Lloyd J ^b   Riggins, Gregory J ^c  

^a J CRAIG VENTER INSTITUTE   (United States)

^b LUDWIG INSTITUTE FOR CANCER RESEARCH   (Australia)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASE CONTROL; DRUG PRODUCTS; DRUG THERAPY; GENES; HEALTH CARE; MUTAGENESIS; TUMORS;

CANCER THERAPIES; ONCOGENOMICS;

BIOMEDICAL ENGINEERING;

ANTINEOPLASTIC AGENT; BEVACIZUMAB; GEMTUZUMAB OZOGAMICIN; IBRITUMOMAB TIUXETAN; IMATINIB; RITUXIMAB; SUNITINIB; TRASTUZUMAB;

CANCER; MEDICINE;

CANCER CHEMOTHERAPY; CANCER GENETICS; GENE MUTATION; GENE SEQUENCE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; REVIEW; SYSTEMATIC REVIEW; TECHNOLOGY;

BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; GENOMICS; HUMANS; NEOPLASMS; ONCOGENES;

EID: 2642549937     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02627     Document Type: Review

References (97)

1. Vogelstein, B. & Kinzler, K. W. The Genetic Basis of Human Cancer (McGraw-Hill, New York, 2002).
2. Balmain A., Gray, J. & Ponder, B. The genetics and genomics of cancer. Nature Genet. 33 (suppl.), 238-244 (2003).
3. Popescu, N. C. Comprehensive genetic analysis of cancer cells. J. Cell. Mol. Med. 4, 151-163 (2000).
4. International Human Genome Sequencing Consolium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
5. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
6. Druker, B. I. STI571 (Gleevec) as a paradigm for cancer therapy. Trends Mol. Med. 8, S14-S18 (2002).
7. Kim, J. A. Targeted therapies for the treatment of cancer. Am. Surg. 186, 264-268 (2003).
8. Smith, I. E. Efficacy and safety of Herceptin in women with metastatic breast cancer; results from pivotal clinical studies. Anticancer Drugs (suppl. 4), S3-S10 (2001).
9. Salgaller, M. Technology evaluation: bevacizumab, Genentech/Roche. Curr. Opin. Mol. Ther. 5, 657-667 (2003).
10. Schadt, E. E., Monks, S. A. & Friend, S. H. A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets. Biochem. Soc. Trans. 31, 437-443 (2003).
11. Fischer, O. M., Streit, S., Hart, S. & Ullrich, A. Beyond Herceptin and Gleevec. Curr. Opin. Chem. Biol. 7, 490-495 (2003).
12. Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949-954 (2002).
13. Bardelli, A. et al. Mutational analysis of the tyrosine kinome in colorectal cancers. Science 300, 949 (2003).
14. Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004).
15. Hilgenfeld, E. et al. Spectral karyotyping in cancer cytogenetics. Methods Mol. Med. 68, 29-44 (2002).
16. Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291-2305 (2003).
17. Cowell, J. K. & Nowak, N. J. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv. Cancer Res. 90, 91-125 (2003).
18. Liang, G. et al. DNA methylation differences associated with tumor tissues identified by genome scanning analysis. Genomics 53, 260-268 (1998).
19. Cottrell, S. E. et al. A real-time PCR assay for DNA-methylation using methylation-specific blockers. Nucleic Acids Res. 32, e10 (2004).
20. Greshock, J. et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res. 14, 179-187 (2004).
21. Wang, T. L. et al. Digital karyotyping. Proc Natl Acad. Sci. USA 99, 16156-16161 (2002).
22. Wang, T. L. et al. Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc. Natl Acad. Sci. USA 101, 3089-3094 (2004).
23. Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA 100, 7696-7701 (2003).
24. Beroud, C. & Soussi, T. The UMD-p53 database: New mutations and analysis tools. Hum. Mutat. 21, 176-181 (2003).
25. Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177-183 (2004).
26. Ramaswamy, S., Ross, K. N., Lander, E. S. & Golub, T. R. A molecular signature of metastasis in primary solid tumors. Nature Genet. 33, 49-54 (2003).
27. Sorlie, T. et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. USA 100, 8418-8423 (2003).
28. Rosenwald, A. et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J. Exp. Med. 198, 851-862 (2003).
29. van't Veer, L. J. et al. Expression profiling predicts outcome in breast cancer. Breast Cancer Res. 5, 57-58 (2003).
30. van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999-2009 (2002).
31. Nutt, C. L. Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res. 63, 1602-1607 (2003).
32. Dyrskjot, L. et al. Identifying distinct classes of bladder carcinoma using microarrays. Nature Genet. 33, 90-96 (2003).
33. Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene-expression. Science 270, 484-487 (1995).
34. Lal, A. et al. A public database for gene expression in human cancers. Cancer Res. 59, 5403-5407 (1999).
35. Buckhaults, P. et al. Identifying tumor origin using a gene expression-based classification map. Cancer Res. 63, 4144-4149 (2003).
36. Jongeneel, C. V. et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc. Natl Acad. Sci. USA 100, 4702-4705 (2003).
37. Brentani, H. et al. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags Proc. Natl Acad. Sci. USA 100, 13418-13423 (2003).
38. Strausberg, R. L. et al. An international database and integrated analysis tools for the study of cancer gene expression. Pharmacogenomics J. 2, 156-164 (2002).
39. Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508-512 (2002).
40. Ota, T. et al. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature Genet. 36, 40-45 (2004).
41. Strausberg, R. L. et al. Generation and initial analysis of more than 15,000 full-length human and mousecDNA sequences. Proc. Natl Acad. Sci. USA 99, 16899-16903 (2002).
42. Xu, Q. & Lee, C. Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res. 31, 5635-5643 (2003).
43. Wang, Z. et al. Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res. 63, 655-657 (2003).
44. Kriventseva, E. V. et al. Increase of functional diversity by alternative splicing. Trends Genet. 19, 124-128 (2003).
45. Strausberg, R. L., Simpson, A. J. & Wooster, R. Sequence-based cancer genomics: progress, lessons and opportunities. Nature Rev. Genet. 4, 409-418 (2003).
46. Drevs, J., Medinger, M., Schmidt-Gersbach, C., Weber, R. & Unger, C. Receptor tyrosine kinases: the main targets for new anticancer therapy. Curr. Drug Targets 4, 113-121 (2003).
47. Sausville, E. A., Elsayed, Y., Monga, M. & Kim, G. Signal transduction - directed cancer treatments. Annu. Rev. Pharmacol. Toxicol. 43, 199-231 (2003).
48. Cockerill, G. S. & Lackey, K. E. Small molecule inhibitors of the class 1 receptor tyrosine kinase family. Curr. Top. Med. Chem. 2, 1001-1010 (2002).
49. Wilhelm, S. & Chien, D. S. BAY 43-9006: preclinical data. Curr. Pharm. Des. 8, 2255-2257 (2002).
50. Joensuu, H. & Dimitrijevic, S. Tyrosine kinase inhibitor imatinib (STI571) as an anticancer agent for solid tumours. Ann. Med. 33, 451-455 (2001).
51. Demetri, G. D. Targeting the molecular pathophysiology of gastrointestinal stromal tumors with imatinib. Mechanisms, successes, and challenges to rational drug development. Hematol. Oncol. Clin. North Am. 16, 1115-1124 (2002).
52. Druker, B. Imatinib mesylate in the treatment of chronic myeloid leukaemia. Expert Opin. Pharmacother. 4, 963-971 (2003).
53. Tipping, A. J. & Melo, J. V. Imatinib mesylate in combination with other chemotherapeutic drugs: In vitro studies. Semin. Hematol. 40, 83-91 (2003).
54. Druker, B. Imatinib alone and in combination for chronic myeloid leukemia. Semin. Hematol. 40, 50-58 (2003).
55. Joensuu, H. et al. Management of malignant gastrointestinal stromal tumours. Lancet Oncol. 3, 655-664 (2002).
56. Joensuu, H. Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor. N. Engl. J. Med. 344, 1052-1056 (2001).
57. GIST SU11248 Study Group. Clinical activity and tolerability of the multi-targeted tyrosine kinase inhibitor SU11248 in patients (pts) with metastatic gastrointestinal stromal tumor (GIST) refractory to imatinib mesylate. Proc. Am. Soc. Clin. Oncol. 22, 814 (abstr. 3273) (2003).
58. Egland, K. A., Vincent, J. J., Strausberg, R., Lee, B. & Pastan, I. Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins. Proc. Natl Acad. Sci. USA 100, 1099-1104 (2003).
59. Olsson, P., Motegi, A., Bera, T. K., Lee, B. & Pastan, I. PRAC2: a new gene expressed in human prostate and prostate cancer. Prostate 56, 123-130 (2003).
60. Jager, D. Identification of a tissue-specific putative transcription factor in breast tissue by serological screening of a breast cancer library. Cancer Res. 61, 2055-2061 (2001).
61. Bera, T. K. NGEP, a gene encoding a membrane protein detected only in prostate cancer and normal prostate. Proc. Natl Acad. Sci. USA 101, 3059-3064 (2004).
62. Scanlan, M. J., Gure, A. O., Jungbluth, A. A., Old, L. J. & Chen, Y. T. Cancer/testis antigens: an expanding family of targets for cancer immunotherapy. Immunol. Rev. 188, 22-32 (2002).
63. Scanlan, M. J., Simpson, A. J. & Old, L. J. The cancer/testis genes: review, standardization, and commentary. Cancer Immun. 4, 1 (2004).
64. Scanlan, M. J. et al. Identification of cancer/testis genes by database mining and mRNA expression analysis. Int. J. Cancer 98, 485-492 (2002).
65. Old, L. J. Cancer/testis (CT) antigens - a new link between gametogenesis and cancer. Cancer Immun. 1, 1 (2001).
66. Durrant, L. G. & Spendlove, I. Cancer vaccines entering Phase III clinical trials. Expert Opin. Emerg. Drugs 8, 489-500 (2003).
67. Jager, E., Jager, D. & Knuth, A. Antigen-specific immunotherapy and cancer vaccines. Int. J. Cancer 106, 817-820 (2003).
68. Albanell, J., Codony, J., Rovira, A., Mellado, B. & Gascon, P. Mechanism of action of anti-HER2 monoclonal antibodies: scientific update on trastuzumab and 2C4. Adv. Exp. Med. Biol. 532, 253-268 (2003).
69. Blackledge, G. & Averbusch, S. Gefitinib ('Iressa', ZD1839) and new epidermal growth factor receptor inhibitors. Br. J. Cancer 90, 566-572 (2004).
70. Coiffier, B. Immunochemotherapy: the new standard in aggressive non-Hodgkin's lymphoma in the elderly. Semin. Oncol. 30, 21-27 (2003).
71. Wannesson, L. & Ghielmini, M. Overview of antibody therapy in B-cell non-Hodgkin's lymphoma. Clin. Lymphoma 4 (suppl. 1), S5-S12 (2003).
72. Jain, R. K. Tumor angiogenesis and accessibility: role of vascular endothelial growth factor. Semin. Oncol. 29, 3-9 (2002).
73. Milenic, D. E. & Brechbiel, M. W. Targeting of radio-isotopes for cancer therapy. Cancer Biol. Ther. 3 (2004).
74. Damle, N. K. & Frost, P. Antibody-targeted chemotherapy with immunoconjugates of calicheamicin. Curr. Opin. Pharmacol. 3, 386-390 (2003).
75. McCormick, F. Cancer-specific viruses and the development of ONYX-015. Cancer Biol. Ther. 2 (suppl. 1), s157-s160 (2003).
76. Tong, A. W., Zhang, Y. A., Cunningham, C., Maples, P. & Nemunaitis, J. Potential clinical application of antioncogene ribozymes for human lung cancer. Clin. Lung Cancer 2, 220-226 (2001).
77. Moon, C., Oh, Y. & Roth, J. A. Current status of gene therapy for lung cancer and head and neck cancer. Clin. Cancer Res. 9, 5055-5067 (2003).
78. McNeish, I. A., Bell, S. J. & Lemoine, N. R. Gene therapy progress and prospects: Cancer gene therapy using tumour suppressor genes. Gene Ther. 11, 497-503 (2004).
79. Torrance, C. J., Agrawal, V., Vogelstein, B. & Kinzler, K. W. Use of isogenic human cancer cells for high-throughput screening and drug discovery. Nature Biotechnol. 19, 940-945 (2001).
80. Strausberg, R. L. & Schreiber, S. L. From knowing to controlling: a path from genomics to drugs using small molecule probes. Science 300, 294-295 (2003).
81. Koehler, A. N., Shamji, A. F. & Schreiber, S. L. Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis. J. Am. Chem. Soc. 125, 8420-8421 (2003).
82. Zerhouni, E. Medicine. The NIH Roadmap. Science 302, 63-72 (2003).
83. Collins, F. S., Morgan, M. & Patrinos, A. The Human Genome Project: lessons from large-scale biology. Science 300, 286-290 (2003).
84. Newman, D. J., Cragg, G. M. & Snader, K. M. Natural products as sources of new drugs over the period 1981-2002. J. Nat. Prod. 66, 1022-1037 (2003).
85. Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853-858 (2000).
86. Brizuela, L., Richardson, A., Marsischky, G. & Labaer, J. The FLEXGene repository: Exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era. Arch. Med. Res. 33, 318-324 (2002).
87. Kretzschmar, T. & von Ruden, T. Antibody discovery: phage display. Curr. Opin. Biotechnol. 13, 598-602 (2002)
88. Brekke, O. H. & Loset, G. A. New technologies in therapeutic antibody development. Curr. Opin. Pharmacol. 3, 544-550 (2003).
89. Pasqualini, R. & Ruoslahti, E. Organ targeting in vivo using phage display peptide libraries. Nature 380, 364-366 (1996).
90. Ellerby, H. M. et al. Anti-cancer activity of targeted pro-apoptotic peptides. Nature Med. 5, 1032-1038 (1999).
91. Scott, A. M. et al. A Phase I dose-escalation study of sibrotuzumab in patients with advanced or metastatic fibroblast activation protein-positive cancer. Clin. Cancer Res. 9, 1639-1647 (2003).
92. Welt, S. et al. Phase I study of anticolon cancer humanized antibody A33. Clin. Cancer Res. 9, 1338-1346 (2003).
93. Scott, A. M. et al. Specific targeting, biodistribution, and lack of immunogenicity of chimeric anti-GD3 monoclonal antibody KM871 in patients with metastatic melanoma: results of a phase I trial. J. Clin. Oncol. 19, 3967-3987 (2001).
94. Jager, E. et al. Induction of primary NY-ESO-1 immunity: CD8+ T lymphocyte and antibody responses in peptide-vaccinated patients with NY-ESO-1+cancers. Proc. Natl Acad. Sci. USA 97, 12198-12203 (2000).
95. Atanackovic, D. Vaccine-induced CD4+ T cell responses to MAGE-3 protein in lung cancer patients. J. Immunol. 172, 3289-3296 (2004).
96. Duyk, G. Attrition and translation. Science 302, 603-605 (2003).
97. Rapisarda, A. et al. Identification of small molecule inhibitors of hypoxia-inducible factor 1 transcriptional activation pathway. Cancer Res. 62, 4316-4324 (2002).