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Genomic screen for epigenetically silenced tumor suppressor genes
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An epigenetic, gene-silencing technology for genomic screening of epigenetically silenced tumor suppressor genes
Inactive Publication Date: 2007-11-28
THE JOHN HOPKINS UNIV SCHOOL OF MEDICINE
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Unfortunately, for most cancers, no such marker molecules are yet available
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Embodiment 1
Identification of epigenetically silenced tumor suppressor genes in esophageal cancer cells
[0130] This example provides a genomic screening method for identifying epigenetically silenced genes associated with esophageal squamous cell carcinoma cells, including epigenetically silenced tumor suppressor genes (See also, Yamashita et al., Cancer Cell 2:485-495, 2002, which is hereby incorporated by reference).
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Cell Lines and Tissue Samples
[0131] Esophageal squamous cell carcinoma (ESCC) cell lines TE1, TE2, TE3, TE4, TE5, TE7, TE13, KYSE30, KYSE70, KYSE110, KYSE140, KYSE150, KYSE200, KYSE410 and KYSE520 were obtained from the Department of Biomedical Research, Department of Aging and Cancer, Tohoku University Obtained from the Cell Response Center (TE series), KYSE series is kindly provided by Dr. Shimada, Department of Surgery, Kyoto University. Cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum for isolation of DNA and RNA. Primary ...
Embodiment 2
Identification of epigenetically silenced tumor suppressor genes in head and neck cancer cells
[0153] This example extends the results published above for esophageal cancer cells to head and neck squamous cell carcinoma (HNSCC) cells.
[0154] HNSCC cells were treated with 10 μM 5Aza-dC or 0.1 μM 5Aza-dC and 300 nM TSA, and the screening method was as described in Example 1. Reactivation of epigenetically silenced genes was found in both groups of treated cells. Exemplary genes had at least a 2-fold increase in expression, as shown in Tables 5 and 6 (the fold increase is shown in the second column).
[0155] These results demonstrate that the genomic screening method disclosed in Example 1 can be extended to other cancer cell types. Further analysis of re-expressed genes in HNSCC cells was performed as disclosed in Example 1, and genes with tumor suppressor activity could be identified.
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Abstract
Methods of genomic screening to identify epigenetically silenced genes, including epigenetically silenced tumor suppressor genes are provided. Also provided are methods of detecting a cancer, for example, an esophageal squamous cell carcinoma or a head and neck squamous cell carcinoma, as are methods of treating a subject having such a cancer.
Description
[0001] This application claims priority under U.S.C. Section 119(e)(1), U.S. Serial No. 60 / 362,577, filed March 7, 2002, the entire contents of which are hereby incorporated by reference. [0002] Portions of this invention were made with government support under grant CA84986-04 from the National Institutes of Health. The US government may therefore have certain rights in this invention. technical field [0003] The present invention may be generally considered to relate to methods of detecting epigenetically silenced tumor suppressor genes in cancer cells, and more particularly to methods of diagnosis and treatment of cancers such as esophageal or head and neck cancers method. Background technique [0004] While cancer is generally thought to be caused by genetic changes such as a mutation in a gene, it is now more clearly recognized that epigenetic mechanisms that do not alter the DNA sequence can also cause cancer. The most common epigenetic change is the silencing of ...
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