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[Cancer Research 63, 2164-2171, May 1, 2003]
© 2003 American Association for Cancer Research

Molecular Biology and Genetics

Triple Analysis of the Cancer Epigenome

An Integrated Microarray System for Assessing Gene Expression, DNA Methylation, and Histone Acetylation1

Huidong Shi, Susan H. Wei, Yu-Wei Leu, Farahnaz Rahmatpanah, Joseph C. Liu, Pearlly S. Yan, Kenneth P. Nephew and Tim Hui-Ming Huang2,3

Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65203 [H. S., S. H. W., Y-W. L., F. R., J. C. L., P. S. Y., T. H-M. H.]; Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana 47405 [K. P. N.]; and Departments of Cellular and Integrative Physiology, and Obstetrics and Gynecology, Indiana University Cancer Center, Indianapolis, Indiana, 46202 [K. P. N.]

We developed a novel microarray system to assess gene expression, DNA methylation, and histone acetylation in parallel, and to dissect the complex hierarchy of epigenetic changes in cancer. An integrated microarray panel consisting of 1507 short CpG island tags located at the 5'-end regions (including the first exons) was used to assess effects of epigenetic treatments on a human epithelial ovarian cancer cell line. Treatment with methylation (5-aza-2'-deoxycytidine) or deacetylation (trichostatin A) inhibitors alone resulted in up-regulation of 1.9 or 1.1% of the genes analyzed; however, the combined treatment resulted in synergistic reactivation of more genes (10.4%; P < 0.001 versus either treatment alone). On the basis of either primary or secondary responses to the treatments, genes were identified as methylation-dependent or -independent. Synergistic reactivation of the methylation-dependent genes by 5-aza-2'-deoxycytidine plus trichostatin A revealed a functional interaction between methylated promoters and deacetylated histones. Increased expression of some methylation-independent genes was associated with enhanced histone acetylation, but up-regulation of most of the genes identified using this technology was because of events downstream of the epigenetic cascade. We demonstrate proof of principle for using the triple microarray system in analyzing the dynamic relationship between transcription factors and promoter targets in cancer genomes.




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HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Cancer Research Clinical Cancer Research
Cancer Epidemiology Biomarkers & Prevention Molecular Cancer Therapeutics
Molecular Cancer Research Cancer Prevention Research
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Copyright © 2003 by the American Association for Cancer Research.