One of the major problems in cancer biology is to define the aberrant pattern of gene expression in tumor cells and to relate this pattern to specific genomic alterations which occur during tumorigenesis. To address this issue, a novel technology, DNA microarray hybridization is being applied to analyze the consequences of chromosome anomalies at the level of gene expression. Using a robotic device, it is possible to print thousands of DNA probes representing the complete genome on a single microscope slide. Fluorescent probes prepared from any cell or tissue source of interest are then hybridized to these arrays providing a large scale view of gene expression. The ultimate goal of this project is genome wide expression analysis. In this fashion, it is proving possible to profile individual diseases, and to determine the consequences of a given genetic alteration on gene expression. This technology is now being applied in model systems carrying alterations in tumor specific genes affected by translocation, activation mutation, amplification or deletion, and in models which have distinct biological properties such as metastasis or responsiveness to hormones. Information obtained from model systems is then integrated with gene expression profiles derived from the statistical analysis of expression data from tissue specimens. Our recent efforts have applied this technology to pediatric cancers, adult sarcomas, melanoma and breast cancers. We have been able to establish the potential of microarrays for the accurate diagnosis of pediatric cancers and for distinguishing estrogen receptor positive breast cancers from receptor negative tumors. Using data from laboratory models we have uncovered patterns of gene expressionrelated to important clinical properties of cancers such as estrogen sensitivity in breast cancer and metastasis in melanoma and osteosarcoma.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Intramural Research (Z01)
Project #
1Z01HG000186-04
Application #
6988871
Study Section
(CGB)
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2004
Total Cost
Indirect Cost
Name
Human Genome Research
Department
Type
DUNS #
City
State
Country
United States
Zip Code
Davis, Sean; Meltzer, Paul S (2006) Ewing's sarcoma: general insights from a rare model. Cancer Cell 9:331-2
Seftor, Elisabeth A; Meltzer, P S; Kirschmann, D A et al. (2006) The epigenetic reprogramming of poorly aggressive melanoma cells by a metastatic microenvironment. J Cell Mol Med 10:174-96
Li, H M; Man, C; Jin, Y et al. (2006) Molecular and cytogenetic changes involved in the immortalization of nasopharyngeal epithelial cells by telomerase. Int J Cancer 119:1567-76
Crawford, Gregory E; Davis, Sean; Scacheri, Peter C et al. (2006) DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods 3:503-9
Scacheri, Peter C; Davis, Sean; Odom, Duncan T et al. (2006) Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet 2:e51
Furumoto, Hiroko; Ying, Hao; Chandramouli, G V R et al. (2005) An unliganded thyroid hormone beta receptor activates the cyclin D1/cyclin-dependent kinase/retinoblastoma/E2F pathway and induces pituitary tumorigenesis. Mol Cell Biol 25:124-35
Moeller, Lars C; Dumitrescu, Alexandra M; Walker, Robert L et al. (2005) Thyroid hormone responsive genes in cultured human fibroblasts. J Clin Endocrinol Metab 90:936-43
Kim, Kyu-Tae; Baird, Kristin; Ahn, Joon-Young et al. (2005) Pim-1 is up-regulated by constitutively activated FLT3 and plays a role in FLT3-mediated cell survival. Blood 105:1759-67
Meltzer, Paul S (2005) Cancer genomics: small RNAs with big impacts. Nature 435:745-6
Amundson, Sally A; Do, Khanh T; Vinikoor, Lisa et al. (2005) Stress-specific signatures: expression profiling of p53 wild-type and -null human cells. Oncogene 24:4572-9

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