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Identification of Epigenetically Silenced Genes in Tumor Endothelial Cells

¹ Department of Pathology, Research Institute for Growth and Development, Maastricht University and University Hospital, Maastricht, the Netherlands; ² Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium; ³ Department of Pathology and Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; ⁴ The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland; and ⁵ Laboratory of Bioinformatics and Computational Genomics, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium

Requests for reprints: Manon van Engeland, Department of Pathology, Research Institute for Growth and Development, Maastricht University and University Hospital, P.O. Box 616, 6200 MD Maastricht, the Netherlands. Phone: 31-43-3874622; Fax: 31-43-3876613; E-mail: m.vanengeland{at}path.unimaas.nl.

Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells. We recently showed that DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors directly repress endothelial cell growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDAC are involved in regulation of endothelial cell gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes down-regulated in tumor-conditioned versus quiescent endothelial cells, and reexpressed by 5-aza-2'-deoxycytidine (DAC) and trichostatin A (TSA). Among the 81 genes identified, 77% harbored a promoter CpG island. Validation of mRNA levels of a subset of genes confirmed significant down-regulation in tumor-conditioned endothelial cells and reactivation by treatment with a combination of DAC and TSA, as well as by both compounds separately. Silencing of these genes in tumor-conditioned endothelial cells correlated with promoter histone H3 deacetylation and loss of H3 lysine 4 methylation, but did not involve DNA methylation of promoter CpG islands. For six genes, down-regulation in microdissected human tumor endothelium was confirmed. Functional validation by RNA interference revealed that clusterin, fibrillin 1, and quiescin Q6 are negative regulators of endothelial cell growth and angiogenesis. In summary, our data identify novel angiogenesis-suppressing genes that become silenced in tumor-conditioned endothelial cells in association with promoter histone modifications and reactivated by DNMT and HDAC inhibitors through reversal of these epigenetic modifications, providing a mechanism for epigenetic regulation of tumor angiogenesis. [Cancer Res 2007;67(9):4138–48]

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